I had the same error message trying to submit an update to a Watch App that was previously rejected. Since i had previously uploaded, I did not see this error. I used a support incident to get help after exhausting all paths.
I got a response in just 1 or 2 business days -- which at first annoyed me. They said i needed to reset everything to use "team provisioning profiles" and all would be fine. I am an individual developer, so my "team profile" is just mine... but I did walk through all the steps and ta-da, much to my surprise, everything worked and the errors went away. Nothing really to do with any of the application specific or other provisioning profiles i had -- i must have changed a "signing identity" somewhere so Xcode's automatic resolution / fix up did not work.
Apple's message was:
CONVERTING TO TEAM BASED CODE SIGNING
Team-based signing should be used in Xcode 5 and later: it’s the recommended workflow and is what’s covered in App Distribution Guide. Team based code signing requires resetting of all code signing settings in each targets build settings to their defaults. Xcode will no longer use the Code Signing Identity and Provisioning Profile build settings, but instead choose the best combination of signing identities and provisioning profile for the scheme being built.
Technical Q&A QA1814 - Setting up Xcode to automatically manage your provisioning profiles
Which is quite clear and solved all my problems.