I had the same issue, with an over-the-air Enterprise app, that was working prior to updating to XCode 6.1.
I ran down the usual suspects (Bundle identifier, a file or directory named "resources", Cleaning and Building, etc.). No dice.
Here's what fixed my issue - I renamed my application's .plist file, and copied in a .plist file from a project that was working fine after the XCode update.
I didn't do a line by line compare to see what changed... because I had already wasted a day on this. Maybe later. But not today.
Hope this helps someone else NOT spend a wasted afternoon.