The iTunes Connect gave this error message to me when I wanted to upload an ipa file to.
Several days I used to have a trouble with that. I found out that it was caused by cocoapods 0.39.0.beta.4. To be more accurate this problem appears when I'm adding some dependencies to a watch extension target. That is the empty folder 'Frameworks' is being created into the appex directory which causes the current issue. Downgrade to 0.38.2 have solved this problem though.

The same behavior is for such combinations
Xcode 6 + watch os 1
Xcode 7 + watch os 1
Xcode 7 + watch os 2

Thanks.