I don't use any FB, Whatsamajigger or some of the others mentioned. It is an incoming comm issue for sure. Phone, (SMS) Messaging and eMail are all stock on my device and they behave this way.
It's a non-issue, IMHO, and here's why I say that... You get a notice in Action Center and you dismiss it. Resets notifications there to zero. Great. Now a new notification will trigger the icon to display at the top of your screen. You don't miss your newest incoming. For whatever reason, you deem the incoming comm as not important enough for immediate viewing - or maybe you are in a meeting or other situation where you CAN'T open the message. The Live Tile reminds you that you need to get back to it. The Live Tile is doing the job it was designed to do. Dismissing a notification in Action Center should NOT reset the counter on the Tile - that would mean marking the message as read. You haven't read it yet. Now if the Tile counter gets reset and you forget you have a message and it's important - you would be upset that Windows failed to remind you of your unread messages!!!
If you find it annoying, I suspect it's because you are using a service that overloads you with comm by it's very nature, like a Facebook or a Twitter. Something that demands constant attention. Something that keeps notifying you so much that you would (almost) never just pop into the messages and clear them as they come in... Whereas with Phone or SMS you are way more likely to want to get to the incoming comm quickly.
It's not the Action Center behavior, it's doing its job. It's not the Live Tile's fault either. It's behaving the way it was designed to do.
Suggestion:
- Settings
- notifications + actions
- tap on the name of App
- Show in Notification Center - toggle to Off
Now you aren't annoyed by the double notification. Otherwise you are asking for the Live Tile count to be broken...