Jonathan suggest here: Xcode Includes .xib files that have been deleted! that cleaning all targets and empty the caches will fix the problem with Xcode including deleted .xi
I have been pulling out hair from my head because I thought that I had the same problem. When building the app I didn't get the same result on my iPhone as on the simulator.
The problem was that I had somehow made a localized version of the MainStoryboard.storyboard file. So when I ran the app on my phone it showed the danish version... and the simulator showed the english version.
Yeah I'm new! :)