I just noticed the same problem on my iPhone5 with iOS 9.3.1 - except the app was Podcast leaving 100's of "New episode is available for podcast {xyz}"
Pressing the X and Clear did nothing - but I did notice that all of the Timestamp entries for each notification began to blink rapidly. Plus the scroll up/down feature became very very slow until I closed the notification menu.
Another thread has a general workaround- which is to toggle the notification settings for "Group By" which has the side effect of clearing the notifications.
https://discussions.apple.com/thread/7250244?tstart=0