I'm having the same issue as this guy, this guy, and this guy (nota bene, I'm actually not sure if they're all guys, per se).
They all ended up finding their own solutions, but none of them apply to my issue. I'm using Xcode 6.1 in my iOS 8 app with an included extension. The app and the extension both rely on an included framework. When I try to submit the app to the Store, the validation warning I get is "ERROR ITMS-9000: Invalid bundle. The bundle at 'xxxxx.appex' contains disallowed file 'Frameworks'".
I can't even find a file called Frameworks. The shared framework is supposed to be saved at /Library/Frameworks, which is Apple's recommended save location. The project also uses Cocoapods, which strikes me as the only other possible culprit, since it has references in its configuration files to $FRAMEWORK_PATH (though the build folder doesn't include a file or folder with that name).