I do:
$ git commit .
$ git push
error: Entry \'file.php\' not uptodate. Cannot merge.
Then I do
$ git pull
Already up-to-date.
I would cut and paste my file.php locally out of the working folder. To your desktop lets say.
Then do a pull, then git should fetch the lastest file.php from the server. Then just paste in your copy of file.php and overwrite the pulled one or open up both versions and just paste in your changes.
I hope that does the trick.