I could not reproduce this predictably, but have seen this happening at least once myself, and there's a report from klobag@. At this point I unfortunately don't have a clue why it's happening.

Found the cause - it happens when user quits PWA while the navigation is in progress. Even though PWA is no longer visible, notification can get shown in after the navigation finishes in order to update the URL - which is a bug.

Fix coming soon.

The following revision refers to this bug:
  https://chromium.googlesource.com/chromium/src.git/+/3a81504d9fe06d98db2161563600ac4a43be1ffe

commit 3a81504d9fe06d98db2161563600ac4a43be1ffe
Author: Piotr Swigon <piotrs@chromium.org>
Date: Tue Oct 10 03:29:46 2017

[WebApps] Update the URL in a notification only if activity is active.

This fixes a bug where a webapp notification could have been shown after
webapp window has been closed. This could have happened if the user
closed the webapp activity while navigation was in progress.

Unfortunately no test, as this is a race condition and test is likely to
be flaky or not effective.

Bug:  772755 
Change-Id: I4987c6a474f0b3d0d55a44d34ecab03f6fecb990
Reviewed-on: https://chromium-review.googlesource.com/708174
Commit-Queue: Piotr Swigon <piotrs@chromium.org>
Reviewed-by: Dominick Ng <dominickn@chromium.org>
Cr-Commit-Position: refs/heads/master@{#507579}
[modify] https://crrev.com/3a81504d9fe06d98db2161563600ac4a43be1ffe/chrome/android/java/src/org/chromium/chrome/browser/webapps/WebappActivity.java

This should no longer happen. Marking as Fixed.