I can't understand why this bug has remained there for so long.
You would expect that during an activity, if you push stop, the timer will stop and the activity paused. This does not happen when there is a notification/alert on the screen. Instead you have to either wait for whatever has popped up to time out, or push the back button before the stop button.
This makes using navigation features a total pain. The stop/start button should work regardless of what's on the screen if you're not say, on the music player screen - it should have priority over everything else. I'm quite sure that it used to work in this way at one time.