A few days ago I got the solution for that from the apple support:
-Open the terminal (applications/Terminal)
-type: mdfind kMDItemAppStoreHasReceipt=1
Example should be something like
Last login: Tue Jul 5 09:04:12 on console
FirstName-LastName-MacBook-Pro:~ firstlastname$ mdfind kMDItemAppStoreHasReceipt=1
/Applications/Evernote.app
/Applications/Twitter.app
/Applications/Install Xcode.app
-compare this list with your purchased apps from the app store
-delete all apps shown in the terminal list but not showed up in the app store list
-restart your Mac, open app store again, the update indicator should now be gone.
After the proceedure everything was fine.
However, not all apps were shown in the terminal list. Some apps I did not buy in the Appstore and I was happy to see that those are not responsible for the bug. I threw out only one application, SolarWalk which a friend send me to check out. I´m not sure if this was a bad egg, however all other apps are running fine.
Hope this helps.