I am unable to install a watchOS 2 WatchKit app due to an application-identifier entitlement. This happened after turning on App Groups in the Capabilities tab.
Full
In my case it was because of the certificate.
because my own certificate to sign the app wasn't part of the developper team (new employee), upgrading the app from the App Store to a new version wasn't allow.
So in case it happen to you and you can't manage to obtain a "good" certificate, just clone the git appStore version, open two Xcode projects, compile the old version, update the settings as you wish, the compile the new one and you're done.
a little bit dirty and tricky but I hope it could help someone.