Right... Do you not think that if you get a notification, say from WhatsApp, and you open it from the Action Centre that you'd want the live tile (and lock screen) notitication to disappear, and vice versa? It just annoys me that I have to see the notification, then re-open the app to clear the notification from the live tile/lock screen, or clear it from the Action Centre despite you already having seen it... Or is it just me?
I'm pretty sure that is exactly how it is supposed to work. Clearing the notification from the action center should remove the notification on the live tile as well, and vice versa. I would imagine that most apps will have to be updated to make that come to fruition.