Since my app launched I have received a few support inquiries of customers who get the "Unable to load <main file>" dialog:
The file <name of fm solution> could not be opened. (Not Found)
The app initially crashes and then it does not write a new copy from the bundle into the documents folder but rather looks to re-open the existing file that was never successfully written in the first place. I don't know if this is due to iOS 9.3.
My only customization is the deletion of the red arrow of the 'slide to cancel graphic' resource to comply with Apple's guidelines. iCloud had to be disabled as well. The app also uses a custom file extension which I have changed back to fm12 on the upcoming release which will hopefully be given the green light by Apple as well. The app works fine when testing on a wide range of device and simulators, Apple tested it for weeks yet customers still experience loading issues.