Resurrecting old thread, but I'm having the same problem on multiple devices.
More specifically, I am updating apps via cable sync from desktop Itunes. The apps are updated on the devices via the cable sync, but the counter stays there. As noted in the original post, when I open app store app on device, the apps needing update will first show Update next to them, then quickly change to Open, but the counter remains.
Iphone 6, iOS 8.1.2
Ipad 2 iOS 8.1.2
Iphone 5 iOS 8.1.2
I called Apple service (my iPhone 6 is still under warranty), they had no clue what was happening. All they did was told me to call them back another day and gave me a case ID.
I have rebooted devices and restored them both as new and from backup. When the restore is done, the counter goes away, but then when a new app needs updating, it happens again.
Anyobody having this issue recently and fixed it? It's very annoying.