IssueTracker

I have a same problem.
Internally, NavController#navigateUp() calls popBackStack().
And popBackStack() calls popBackStack(currentDestination.id, inclusive=true).

    public boolean popBackStack() {
        if (mBackStack.isEmpty()) {
            // Nothing to pop if the back stack is empty
            return false;
        }
        // Pop just the current destination off the stack
        return popBackStack(getCurrentDestination().getId(), true);   <--- this is cause.
    }

So I think,
this problem can't be fixed without navigation cmpt. modification. :(

Component used: Navigation
Version used: 1.0.0-alpha09

But on alpha09 version, popBackStack() is implemented differently.

    public boolean popBackStack() {
        if (mBackStack.isEmpty()) {
            throw new IllegalArgumentException("NavController back stack is empty");
        }
        boolean popped = false;
        while (!mBackStack.isEmpty()) {
            popped = mBackStack.removeLast().getNavigator().popBackStack();  <------ different
            if (popped) {
                break;
            }
        }
        return popped;
    }

Please restore to the upper codes. Or create a new option. :)

I found the commit.
(https://android.googlesource.com/platform/frameworks/support/+/40067518406a59880b0dc47d3f6705b5d15e28fc%5E%21)

Project: platform/frameworks/support
Branch: androidx-master-dev

commit 45818ac652ba3a43b07f980cf22ab78be886d81d
Author: Ian Lake <ilake@google.com>
Date:   Wed Jan 30 10:45:37 2019

    Ensure that popBackStack() only pops one Fragment
   
    When two Fragments with the same destination ID are
    both added to the back stack, they previously had an
    identical back stack name in FragmentManager, which
    incorrectly means that popBackStack with that name
    would pop both off the back stack.
   
    By changing how we generate back stack names for
    FragmentNavigator, we ensure that each back stack
    name is unique and that only one Fragment will be
    popped for each popBackStack() call.
   
    Test: new FragmentNavigatorTest test
    Change-Id: I26bdaeb65620001a74165a166aa74fe48cb468e6
    Fixes: 123552990

M       navigation/fragment/src/androidTest/java/androidx/navigation/fragment/FragmentNavigatorTest.kt
M       navigation/fragment/src/main/java/androidx/navigation/fragment/FragmentNavigator.java

https://android-review.googlesource.com/890733
https://goto.google.com/android-sha1/45818ac652ba3a43b07f980cf22ab78be886d81d

This was regression introduced when fixing https://issuetracker.google.com/issues/110893637 - it is now fixed internally and will be available in the next release of Navigation.