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. :)