My App is in the App store and a new version is in TestFlight. If you have submitted the App to TestFlight, you may have to delete the App from your iPhone and then you will be able to run it again from Xcode. I had the same message after downloading My App from TestFlight, I deleted the TestFlight version and was able to run my App through Xcode.
Hope this helps
Topic:
Developer Tools & Services
SubTopic:
Xcode
Tags: