I have the same FileMerge warning in Git. When I look inside Xcode’s preferences, I can see that neither the iPhoneSimulator nor the iPhoneOS platforms are installed but the directories do exist when I look into “/Applications/Xcode.app/Contents/Developer/Platforms”.
I don’t develop for iOS, so I deleted both iPhoneOS.platform and iPhoneSimulator.platform and the warning went away.
If you do need those platforms, try to reinstall them properly from Xcode.