It really bugged to never have a clean git repo just because of a .DS_Store sitting in the themes directory. .DS_Store files are generated by Mac OS X and are virtually impossible to remove. As it hurts nobody I'd suggest to add .DS_Store to the .gitignore so that the repo keeps clean (better for updates, too).
Added .DS_Store to the .gitignore.
You could always configure a global .gitignore.
See: Ignoring files