Thanks for reporting, would you be able to provide a reproducible case for when this incremental error occurs? The task for merging java resources has multiple incremental inputs depending on where the java resource originates - providing a sample project where this issue can be triggered will help the team narrow what task input is impacted. A longer stacktrace of the issue from #1 might also be useful.

Unfortunately I cannot reproduce it consistently. In fact I don't even know what triggers it (it seems to be some combination of changes).

Like I mentioned above, my hunch is that this is due to having several modules with the same name (impl). The resource in question (impl_debug.kotlin_module) contains the name of the Gradle module and it likely means that there will be conflicts since there are several modules with the same name.

The stack trace looks like this:

org.gradle.api.tasks.TaskExecutionException: Execution failed for task ':app:mergeDebugJavaResource'.	
	at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.lambda$executeIfValid$1(ExecuteActionsTaskExecuter.java:149)	
	at org.gradle.internal.Try$Failure.ifSuccessfulOrElse(Try.java:282)	
	at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeIfValid(ExecuteActionsTaskExecuter.java:147)	
	at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.execute(ExecuteActionsTaskExecuter.java:135)	
	at org.gradle.api.internal.tasks.execution.FinalizePropertiesTaskExecuter.execute(FinalizePropertiesTaskExecuter.java:46)	
	at org.gradle.api.internal.tasks.execution.ResolveTaskExecutionModeExecuter.execute(ResolveTaskExecutionModeExecuter.java:51)	
	at org.gradle.api.internal.tasks.execution.SkipTaskWithNoActionsExecuter.execute(SkipTaskWithNoActionsExecuter.java:57)	
	at org.gradle.api.internal.tasks.execution.SkipOnlyIfTaskExecuter.execute(SkipOnlyIfTaskExecuter.java:74)	
	at org.gradle.api.internal.tasks.execution.CatchExceptionTaskExecuter.execute(CatchExceptionTaskExecuter.java:36)	
	at org.gradle.api.internal.tasks.execution.EventFiringTaskExecuter$1.executeTask(EventFiringTaskExecuter.java:77)	
	at org.gradle.api.internal.tasks.execution.EventFiringTaskExecuter$1.call(EventFiringTaskExecuter.java:55)	
	at org.gradle.api.internal.tasks.execution.EventFiringTaskExecuter$1.call(EventFiringTaskExecuter.java:52)	
	at org.gradle.internal.operations.DefaultBuildOperationRunner$CallableBuildOperationWorker.execute(DefaultBuildOperationRunner.java:204)	
	at org.gradle.internal.operations.DefaultBuildOperationRunner$CallableBuildOperationWorker.execute(DefaultBuildOperationRunner.java:199)	
	at org.gradle.internal.operations.DefaultBuildOperationRunner$2.execute(DefaultBuildOperationRunner.java:66)	
	at org.gradle.internal.operations.DefaultBuildOperationRunner$2.execute(DefaultBuildOperationRunner.java:59)	
	at org.gradle.internal.operations.DefaultBuildOperationRunner.execute(DefaultBuildOperationRunner.java:157)	
	at org.gradle.internal.operations.DefaultBuildOperationRunner.execute(DefaultBuildOperationRunner.java:59)	
	at org.gradle.internal.operations.DefaultBuildOperationRunner.call(DefaultBuildOperationRunner.java:53)	
	at org.gradle.internal.operations.DefaultBuildOperationExecutor.call(DefaultBuildOperationExecutor.java:73)	
	at org.gradle.api.internal.tasks.execution.EventFiringTaskExecuter.execute(EventFiringTaskExecuter.java:52)	
	at org.gradle.execution.plan.LocalTaskNodeExecutor.execute(LocalTaskNodeExecutor.java:42)	
	at org.gradle.execution.taskgraph.DefaultTaskExecutionGraph$InvokeNodeExecutorsAction.execute(DefaultTaskExecutionGraph.java:337)	
	at org.gradle.execution.taskgraph.DefaultTaskExecutionGraph$InvokeNodeExecutorsAction.execute(DefaultTaskExecutionGraph.java:324)	
	at org.gradle.execution.taskgraph.DefaultTaskExecutionGraph$BuildOperationAwareExecutionAction.execute(DefaultTaskExecutionGraph.java:317)	
	at org.gradle.execution.taskgraph.DefaultTaskExecutionGraph$BuildOperationAwareExecutionAction.execute(DefaultTaskExecutionGraph.java:303)	
	at org.gradle.execution.plan.DefaultPlanExecutor$ExecutorWorker.execute(DefaultPlanExecutor.java:463)	
	at org.gradle.execution.plan.DefaultPlanExecutor$ExecutorWorker.run(DefaultPlanExecutor.java:380)	
	at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:64)	
	at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:49)	
Caused by: org.gradle.workers.internal.DefaultWorkerExecutor$WorkExecutionException: A failure occurred while executing com.android.build.gradle.internal.tasks.MergeJavaResWorkAction	
	at org.gradle.workers.internal.DefaultWorkerExecutor$WorkItemExecution.waitForCompletion(DefaultWorkerExecutor.java:283)	
	at org.gradle.internal.work.DefaultAsyncWorkTracker.lambda$waitForItemsAndGatherFailures$2(DefaultAsyncWorkTracker.java:130)	
	at org.gradle.internal.Factories$1.create(Factories.java:31)	
	at org.gradle.internal.work.DefaultWorkerLeaseService.withoutLocks(DefaultWorkerLeaseService.java:321)	
	at org.gradle.internal.work.DefaultWorkerLeaseService.withoutLocks(DefaultWorkerLeaseService.java:304)	
	at org.gradle.internal.work.DefaultWorkerLeaseService.withoutLock(DefaultWorkerLeaseService.java:309)	
	at org.gradle.internal.work.DefaultAsyncWorkTracker.waitForItemsAndGatherFailures(DefaultAsyncWorkTracker.java:126)	
	at org.gradle.internal.work.DefaultAsyncWorkTracker.waitForItemsAndGatherFailures(DefaultAsyncWorkTracker.java:92)	
	at org.gradle.internal.work.DefaultAsyncWorkTracker.waitForAll(DefaultAsyncWorkTracker.java:78)	
	at org.gradle.internal.work.DefaultAsyncWorkTracker.waitForCompletion(DefaultAsyncWorkTracker.java:66)	
	at org.gradle.api.internal.tasks.execution.TaskExecution$3.run(TaskExecution.java:250)	
	at org.gradle.internal.operations.DefaultBuildOperationRunner$1.execute(DefaultBuildOperationRunner.java:29)	
	at org.gradle.internal.operations.DefaultBuildOperationRunner$1.execute(DefaultBuildOperationRunner.java:26)	
	at org.gradle.internal.operations.DefaultBuildOperationRunner$2.execute(DefaultBuildOperationRunner.java:66)	
	at org.gradle.internal.operations.DefaultBuildOperationRunner$2.execute(DefaultBuildOperationRunner.java:59)	
	at org.gradle.internal.operations.DefaultBuildOperationRunner.execute(DefaultBuildOperationRunner.java:157)	
	at org.gradle.internal.operations.DefaultBuildOperationRunner.execute(DefaultBuildOperationRunner.java:59)	
	at org.gradle.internal.operations.DefaultBuildOperationRunner.run(DefaultBuildOperationRunner.java:47)	
	at org.gradle.internal.operations.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:68)	
	at org.gradle.api.internal.tasks.execution.TaskExecution.executeAction(TaskExecution.java:227)	
	at org.gradle.api.internal.tasks.execution.TaskExecution.executeActions(TaskExecution.java:210)	
	at org.gradle.api.internal.tasks.execution.TaskExecution.executeWithPreviousOutputFiles(TaskExecution.java:193)	
	at org.gradle.api.internal.tasks.execution.TaskExecution.execute(TaskExecution.java:166)	
	at org.gradle.internal.execution.steps.ExecuteStep.executeInternal(ExecuteStep.java:105)	
	at org.gradle.internal.execution.steps.ExecuteStep.access$000(ExecuteStep.java:44)	
	at org.gradle.internal.execution.steps.ExecuteStep$1.call(ExecuteStep.java:59)	
	at org.gradle.internal.execution.steps.ExecuteStep$1.call(ExecuteStep.java:56)	
	at org.gradle.internal.operations.DefaultBuildOperationRunner$CallableBuildOperationWorker.execute(DefaultBuildOperationRunner.java:204)	
	at org.gradle.internal.operations.DefaultBuildOperationRunner$CallableBuildOperationWorker.execute(DefaultBuildOperationRunner.java:199)	
	at org.gradle.internal.operations.DefaultBuildOperationRunner$2.execute(DefaultBuildOperationRunner.java:66)	
	at org.gradle.internal.operations.DefaultBuildOperationRunner$2.execute(DefaultBuildOperationRunner.java:59)	
	at org.gradle.internal.operations.DefaultBuildOperationRunner.execute(DefaultBuildOperationRunner.java:157)	
	at org.gradle.internal.operations.DefaultBuildOperationRunner.execute(DefaultBuildOperationRunner.java:59)	
	at org.gradle.internal.operations.DefaultBuildOperationRunner.call(DefaultBuildOperationRunner.java:53)	
	at org.gradle.internal.operations.DefaultBuildOperationExecutor.call(DefaultBuildOperationExecutor.java:73)	
	at org.gradle.internal.execution.steps.ExecuteStep.execute(ExecuteStep.java:56)	
	at org.gradle.internal.execution.steps.ExecuteStep.execute(ExecuteStep.java:44)	
	at org.gradle.internal.execution.steps.RemovePreviousOutputsStep.execute(RemovePreviousOutputsStep.java:67)	
	at org.gradle.internal.execution.steps.RemovePreviousOutputsStep.execute(RemovePreviousOutputsStep.java:37)	
	at org.gradle.internal.execution.steps.CancelExecutionStep.execute(CancelExecutionStep.java:41)	
	at org.gradle.internal.execution.steps.TimeoutStep.executeWithoutTimeout(TimeoutStep.java:74)	
	at org.gradle.internal.execution.steps.TimeoutStep.execute(TimeoutStep.java:55)	
	at org.gradle.internal.execution.steps.CreateOutputsStep.execute(CreateOutputsStep.java:50)	
	at org.gradle.internal.execution.steps.CreateOutputsStep.execute(CreateOutputsStep.java:28)	
	at org.gradle.internal.execution.steps.CaptureStateAfterExecutionStep.executeDelegateBroadcastingChanges(CaptureStateAfterExecutionStep.java:100)	
	at org.gradle.internal.execution.steps.CaptureStateAfterExecutionStep.execute(CaptureStateAfterExecutionStep.java:72)	
	at org.gradle.internal.execution.steps.CaptureStateAfterExecutionStep.execute(CaptureStateAfterExecutionStep.java:50)	
	at org.gradle.internal.execution.steps.ResolveInputChangesStep.execute(ResolveInputChangesStep.java:40)	
	at org.gradle.internal.execution.steps.ResolveInputChangesStep.execute(ResolveInputChangesStep.java:29)	
	at org.gradle.internal.execution.steps.BuildCacheStep.executeWithoutCache(BuildCacheStep.java:166)	
	at org.gradle.internal.execution.steps.BuildCacheStep.lambda$execute$1(BuildCacheStep.java:70)	
	at org.gradle.internal.Either$Right.fold(Either.java:175)	
	at org.gradle.internal.execution.caching.CachingState.fold(CachingState.java:59)	
	at org.gradle.internal.execution.steps.BuildCacheStep.execute(BuildCacheStep.java:68)	
	at org.gradle.internal.execution.steps.BuildCacheStep.execute(BuildCacheStep.java:46)	
	at org.gradle.internal.execution.steps.StoreExecutionStateStep.execute(StoreExecutionStateStep.java:36)	
	at org.gradle.internal.execution.steps.StoreExecutionStateStep.execute(StoreExecutionStateStep.java:25)	
	at org.gradle.internal.execution.steps.RecordOutputsStep.execute(RecordOutputsStep.java:36)	
	at org.gradle.internal.execution.steps.RecordOutputsStep.execute(RecordOutputsStep.java:22)	
	at org.gradle.internal.execution.steps.SkipUpToDateStep.executeBecause(SkipUpToDateStep.java:91)	
	at org.gradle.internal.execution.steps.SkipUpToDateStep.lambda$execute$2(SkipUpToDateStep.java:55)	
	at org.gradle.internal.execution.steps.SkipUpToDateStep.execute(SkipUpToDateStep.java:55)	
	at org.gradle.internal.execution.steps.SkipUpToDateStep.execute(SkipUpToDateStep.java:37)	
	at org.gradle.internal.execution.steps.ResolveChangesStep.execute(ResolveChangesStep.java:65)	
	at org.gradle.internal.execution.steps.ResolveChangesStep.execute(ResolveChangesStep.java:36)	
	at org.gradle.internal.execution.steps.legacy.MarkSnapshottingInputsFinishedStep.execute(MarkSnapshottingInputsFinishedStep.java:37)	
	at org.gradle.internal.execution.steps.legacy.MarkSnapshottingInputsFinishedStep.execute(MarkSnapshottingInputsFinishedStep.java:27)	
	at org.gradle.internal.execution.steps.ResolveCachingStateStep.execute(ResolveCachingStateStep.java:76)	
	at org.gradle.internal.execution.steps.ResolveCachingStateStep.execute(ResolveCachingStateStep.java:37)	
	at org.gradle.internal.execution.steps.ValidateStep.execute(ValidateStep.java:94)	
	at org.gradle.internal.execution.steps.ValidateStep.execute(ValidateStep.java:49)	
	at org.gradle.internal.execution.steps.CaptureStateBeforeExecutionStep.execute(CaptureStateBeforeExecutionStep.java:71)	
	at org.gradle.internal.execution.steps.CaptureStateBeforeExecutionStep.execute(CaptureStateBeforeExecutionStep.java:45)	
	at org.gradle.internal.execution.steps.SkipEmptyWorkStep.executeWithNonEmptySources(SkipEmptyWorkStep.java:177)	
	at org.gradle.internal.execution.steps.SkipEmptyWorkStep.execute(SkipEmptyWorkStep.java:81)	
	at org.gradle.internal.execution.steps.SkipEmptyWorkStep.execute(SkipEmptyWorkStep.java:53)	
	at org.gradle.internal.execution.steps.RemoveUntrackedExecutionStateStep.execute(RemoveUntrackedExecutionStateStep.java:32)	
	at org.gradle.internal.execution.steps.RemoveUntrackedExecutionStateStep.execute(RemoveUntrackedExecutionStateStep.java:21)	
	at org.gradle.internal.execution.steps.legacy.MarkSnapshottingInputsStartedStep.execute(MarkSnapshottingInputsStartedStep.java:38)	
	at org.gradle.internal.execution.steps.LoadPreviousExecutionStateStep.execute(LoadPreviousExecutionStateStep.java:36)	
	at org.gradle.internal.execution.steps.LoadPreviousExecutionStateStep.execute(LoadPreviousExecutionStateStep.java:23)	
	at org.gradle.internal.execution.steps.CleanupStaleOutputsStep.execute(CleanupStaleOutputsStep.java:75)	
	at org.gradle.internal.execution.steps.CleanupStaleOutputsStep.execute(CleanupStaleOutputsStep.java:41)	
	at org.gradle.internal.execution.steps.AssignWorkspaceStep.lambda$execute$0(AssignWorkspaceStep.java:32)	
	at org.gradle.api.internal.tasks.execution.TaskExecution$4.withWorkspace(TaskExecution.java:287)	
	at org.gradle.internal.execution.steps.AssignWorkspaceStep.execute(AssignWorkspaceStep.java:30)	
	at org.gradle.internal.execution.steps.AssignWorkspaceStep.execute(AssignWorkspaceStep.java:21)	
	at org.gradle.internal.execution.steps.IdentityCacheStep.execute(IdentityCacheStep.java:37)	
	at org.gradle.internal.execution.steps.IdentityCacheStep.execute(IdentityCacheStep.java:27)	
	at org.gradle.internal.execution.steps.IdentifyStep.execute(IdentifyStep.java:47)	
	at org.gradle.internal.execution.steps.IdentifyStep.execute(IdentifyStep.java:34)	
	at org.gradle.internal.execution.impl.DefaultExecutionEngine$1.execute(DefaultExecutionEngine.java:64)	
	at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeIfValid(ExecuteActionsTaskExecuter.java:146)	
	at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.execute(ExecuteActionsTaskExecuter.java:135)	
	at org.gradle.api.internal.tasks.execution.FinalizePropertiesTaskExecuter.execute(FinalizePropertiesTaskExecuter.java:46)	
	at org.gradle.api.internal.tasks.execution.ResolveTaskExecutionModeExecuter.execute(ResolveTaskExecutionModeExecuter.java:51)	
	at org.gradle.api.internal.tasks.execution.SkipTaskWithNoActionsExecuter.execute(SkipTaskWithNoActionsExecuter.java:57)	
	at org.gradle.api.internal.tasks.execution.SkipOnlyIfTaskExecuter.execute(SkipOnlyIfTaskExecuter.java:74)	
	at org.gradle.api.internal.tasks.execution.CatchExceptionTaskExecuter.execute(CatchExceptionTaskExecuter.java:36)	
	at org.gradle.api.internal.tasks.execution.EventFiringTaskExecuter$1.executeTask(EventFiringTaskExecuter.java:77)	
	at org.gradle.api.internal.tasks.execution.EventFiringTaskExecuter$1.call(EventFiringTaskExecuter.java:55)	
	at org.gradle.api.internal.tasks.execution.EventFiringTaskExecuter$1.call(EventFiringTaskExecuter.java:52)	
	at org.gradle.internal.operations.DefaultBuildOperationRunner$CallableBuildOperationWorker.execute(DefaultBuildOperationRunner.java:204)	
	at org.gradle.internal.operations.DefaultBuildOperationRunner$CallableBuildOperationWorker.execute(DefaultBuildOperationRunner.java:199)	
	at org.gradle.internal.operations.DefaultBuildOperationRunner$2.execute(DefaultBuildOperationRunner.java:66)	
	at org.gradle.internal.operations.DefaultBuildOperationRunner$2.execute(DefaultBuildOperationRunner.java:59)	
	at org.gradle.internal.operations.DefaultBuildOperationRunner.execute(DefaultBuildOperationRunner.java:157)	
	at org.gradle.internal.operations.DefaultBuildOperationRunner.execute(DefaultBuildOperationRunner.java:59)	
	at org.gradle.internal.operations.DefaultBuildOperationRunner.call(DefaultBuildOperationRunner.java:53)	
	at org.gradle.internal.operations.DefaultBuildOperationExecutor.call(DefaultBuildOperationExecutor.java:73)	
	at org.gradle.api.internal.tasks.execution.EventFiringTaskExecuter.execute(EventFiringTaskExecuter.java:52)	
	at org.gradle.execution.plan.LocalTaskNodeExecutor.execute(LocalTaskNodeExecutor.java:42)	
	at org.gradle.execution.taskgraph.DefaultTaskExecutionGraph$InvokeNodeExecutorsAction.execute(DefaultTaskExecutionGraph.java:337)	
	at org.gradle.execution.taskgraph.DefaultTaskExecutionGraph$InvokeNodeExecutorsAction.execute(DefaultTaskExecutionGraph.java:324)	
	at org.gradle.execution.taskgraph.DefaultTaskExecutionGraph$BuildOperationAwareExecutionAction.execute(DefaultTaskExecutionGraph.java:317)	
	at org.gradle.execution.taskgraph.DefaultTaskExecutionGraph$BuildOperationAwareExecutionAction.execute(DefaultTaskExecutionGraph.java:303)	
	at org.gradle.execution.plan.DefaultPlanExecutor$ExecutorWorker.execute(DefaultPlanExecutor.java:463)	
	at org.gradle.execution.plan.DefaultPlanExecutor$ExecutorWorker.run(DefaultPlanExecutor.java:380)	
	at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:64)	
	at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:49)	
Caused by: java.lang.IllegalStateException: Unexpected combination of states CHANGED, REMOVED for file /path/to/module/build/intermediates/java_res/debug/out/META-INF/impl_debug.kotlin_module	
	at com.android.build.gradle.internal.tasks.IncrementalFileMergerTaskUtils.collectChanges(IncrementalFileMergerTaskUtils.kt:275)	
	at com.android.build.gradle.internal.tasks.IncrementalFileMergerTaskUtils.toInputs(IncrementalFileMergerTaskUtils.kt:229)	
	at com.android.build.gradle.internal.tasks.MergeJavaResWorkAction.run(MergeJavaResWorkAction.kt:68)	
	at com.android.build.gradle.internal.profile.ProfileAwareWorkAction.execute(ProfileAwareWorkAction.kt:74)	
	at org.gradle.workers.internal.DefaultWorkerServer.execute(DefaultWorkerServer.java:63)	
	at org.gradle.workers.internal.NoIsolationWorkerFactory$1$1.create(NoIsolationWorkerFactory.java:66)	
	at org.gradle.workers.internal.NoIsolationWorkerFactory$1$1.create(NoIsolationWorkerFactory.java:62)	
	at org.gradle.internal.classloader.ClassLoaderUtils.executeInClassloader(ClassLoaderUtils.java:100)	
	at org.gradle.workers.internal.NoIsolationWorkerFactory$1.lambda$execute$0(NoIsolationWorkerFactory.java:62)	
	at org.gradle.workers.internal.AbstractWorker$1.call(AbstractWorker.java:44)	
	at org.gradle.workers.internal.AbstractWorker$1.call(AbstractWorker.java:41)	
	at org.gradle.internal.operations.DefaultBuildOperationRunner$CallableBuildOperationWorker.execute(DefaultBuildOperationRunner.java:204)	
	at org.gradle.internal.operations.DefaultBuildOperationRunner$CallableBuildOperationWorker.execute(DefaultBuildOperationRunner.java:199)	
	at org.gradle.internal.operations.DefaultBuildOperationRunner$2.execute(DefaultBuildOperationRunner.java:66)	
	at org.gradle.internal.operations.DefaultBuildOperationRunner$2.execute(DefaultBuildOperationRunner.java:59)	
	at org.gradle.internal.operations.DefaultBuildOperationRunner.execute(DefaultBuildOperationRunner.java:157)	
	at org.gradle.internal.operations.DefaultBuildOperationRunner.execute(DefaultBuildOperationRunner.java:59)	
	at org.gradle.internal.operations.DefaultBuildOperationRunner.call(DefaultBuildOperationRunner.java:53)	
	at org.gradle.internal.operations.DefaultBuildOperationExecutor.call(DefaultBuildOperationExecutor.java:73)	
	at org.gradle.workers.internal.AbstractWorker.executeWrappedInBuildOperation(AbstractWorker.java:41)	
	at org.gradle.workers.internal.NoIsolationWorkerFactory$1.execute(NoIsolationWorkerFactory.java:59)	
	at org.gradle.workers.internal.DefaultWorkerExecutor.lambda$submitWork$0(DefaultWorkerExecutor.java:169)	
	at org.gradle.internal.work.DefaultConditionalExecutionQueue$ExecutionRunner.runExecution(DefaultConditionalExecutionQueue.java:187)	
	at org.gradle.internal.work.DefaultConditionalExecutionQueue$ExecutionRunner.access$700(DefaultConditionalExecutionQueue.java:120)	
	at org.gradle.internal.work.DefaultConditionalExecutionQueue$ExecutionRunner$1.run(DefaultConditionalExecutionQueue.java:162)	
	at org.gradle.internal.Factories$1.create(Factories.java:31)	
	at org.gradle.internal.work.DefaultWorkerLeaseService.withLocks(DefaultWorkerLeaseService.java:249)	
	at org.gradle.internal.work.DefaultWorkerLeaseService.runAsWorkerThread(DefaultWorkerLeaseService.java:109)	
	at org.gradle.internal.work.DefaultWorkerLeaseService.runAsWorkerThread(DefaultWorkerLeaseService.java:114)	
	at org.gradle.internal.work.DefaultConditionalExecutionQueue$ExecutionRunner.runBatch(DefaultConditionalExecutionQueue.java:157)	
	at org.gradle.internal.work.DefaultConditionalExecutionQueue$ExecutionRunner.run(DefaultConditionalExecutionQueue.java:126)	
	... 2 more

Thanks for the additional information. I have refactored the Java Resource merging incremental handling to better handle source file path roots - so hopefully this is enough to eliminate the possibility of collisions between java resources. However, it would be great to test these changes resolve your issue. My current assumption is that the issue occurs when there is a library structure where there are two modules of the same name nested within two differently named modules such as:

app
foo_lib
  foo
bar_lib
  foo

Could you confirm that this setup is similar in your project or if not, can you please provide your project structure or even a project if possible?