For me, I copied a folder into Xcode 4.6.2 with the name “Resources”. When Xcode asked, I created the folder references for any added folders.
Every time I did this, I would have to goto the Derived applications directory, and delete the build directory for my project to get it working again.
Solution: Do not copy a folder by reference into Xcode with the name “Resources”. Rename it to something else other than Resources.
Very annoying error.