I'm on Dev Prev Update 1 (no Cyan) and I have the same issue: when I dismiss all the notification (let's say of Facebook Messenger), I still see the little number in the live tile.
Also, is it normal that once multiple notifications appear they aren't automatically deleted when you read the last message? This would be very useful for FB Messenger, Viber etc: when someone sends you more messages and you click on one notification, you open the app but all the other notifications remain in the action center.
SO: 8.10.14157.200