They are not out of date, this just show you the latest commit date/message related to the file/directory.
After I switched from using WAV files to MP3 files all of my WAV files are still in the other directory, and they are not in the other.
Another strange issue is that only fetch works for me, not pull, and for my friend, vice versa.
Your local copy is probably messed up.
Every project should have a git url. Something like firstname.lastname@example.org:username/projectname.git.. Go to another folder, then do git clone email@example.com:username/projectname.git. git will create a new folder called projectname. If you go to that folder, you should see the same directory structure as the one you see on github.
Start cleaning up your project from this folder. You should read http://git-scm.com/documentation.