When you add a file by selecting "link existing file..." in one of the library folder then save the project and close it down. Open that project up. You get a copy of the linked file and a physical copy of the file in same project.
It seems harmless at first but there are issues arising later on.
It will crash once you export it and run it in Xcode given it doesn’t like 2 files of the same name.
The solution to fix that is easy; simply delete the linked version.
Problem with that is any dependencies to the linked version will be lost and that end up causing a big problem due to having to figure out which files were referencing the linked version.
I'll do a screen dump later on if I get it reappearing again.
Comments
I believe this was the only way to add files in the old days (you added any files using "link files") but then later on they changed the file system to what it is today. So it may be more of a legacy thing than a feature we should use.