I don't know if that's a common problem. Most of the times that we pull a CSS file from our development repo, GIT conflicts with the current file, entirely merging the two files by putting the ">>>" and "<<<" markers at the very top and bottom, and a "===" marker separating them.
We tried some different indentation, and that helped a little, but there's no success at all. We don't have problems with any other file type, most of them are PHP and JS code, in this case.
If that helps, we have set all the text editors on production to use CRLF.
Thanks.