Old question, but now Xcode 7 GM is out, and this behavior hasn't changed, I took a deeper look. The issue, I believe is that code coverage of the test app target is conflicting with code coverage of the main target.
Assuming you don't actually care about code coverage of your test target these settings stop the errors for me, with no need for extra scripts or deleting files:
In your main target (be it a framework, or an app) set:
Enable Code Coverage Support to YES
Generage Legacy Test Coverage Files to YES
Instrument Program Flow to YES
For my purposes I only did this for Debug builds, but your needs may vary.
Then in your Tests target set:
Enable Code Coverage Support to NO
Generage Legacy Test Coverage Files to NO
Instrument Program Flow to NO
This has resolved the error messages, and still allowed the code coverage files to be created appropriately.
Again, the question is old, but as the error still is issued in XCode 7, I found this solution works better than deleting files with special scripts.