This could be a bug in the Android sandbox on the Chromebook since one would think it would stop the app but doesn't. It appears you can "fix" the problem by using the Android settings app to force quit the app:
However, the real question is how it is ending up in this state to begin with. When you close the app window, it should stop the app as a whole. Unless you've written an infinite loop in your project, I don't see any reason the app shouldn't just quit in the normal way when closed.