I have the same issue. Running the GM build from last week before I did the OTA I had 10 updates.
When I updated to the current release it showed I still had 10 updates. Yet in the App Store tab it shows the updates then flickered to open rather than update. Only way I managed to update them was to quickly open and tap update before it changed to open
I have the same thing. 10 apps to update. But they say update for only a second then OPEN. Badge stays at 10.
It seems Twitter might have updated but not sure.
I guess I'm not sure what you guys are having trouble with? I have a handful of apps that for whatever reason with iOS 9 betas, the GM, 9.1 and even the 'new' 9.0 - after installing fresh and restoring my content, some apps just didn't restore...and the App Store for a while was showing some crazy number in the badge, despite there being no updates available after checking. I realized going into purchases and manually tapping the cloud icon for those apps that failed to restore then forced them to download, and shortly after the App Store badge finally disappeared.
Thank god it's not just me! My iPad has 9.1 and now as of today can't get app updates. My iPhone is on 9.0 and can't now either. Apple has to be doing something.