Got this error in xcode 8.0 with a git repository. Wanted to split code into a different file - so duplicated the file, added it to the project and then removed most code from the original file. At this point XCode showed an 'i' (missing file) in the project navigator but compiling the project works fine.
You can't commit with xcode however since it will show the "missing" file as non-existent in the commit-dialog (even though it is clearly there, selectable and editable in the project navigator).
Easy fix was to just commit all changes externally with sourcetree. The moment it was committed, everything worked fine again in xcode.