If you clear notifications in Action Center, it should clear the live tile notification and counter too. But it keeps showing it as if nothing happened. It should be cleared from the tile as well. Developers should report this behavior to Microsoft.
it does clear the live tiles for some apps for me (ativ s)
Did you open the app from Action Center or Live Tile? I said clearing notifications without opening the app. Maybe developers need to update their apps. So it does work. I thought Microsoft forgot to add this functionality. Does not work for Whatsapp.