I do:
$ git commit .
$ git push
error: Entry \'file.php\' not uptodate. Cannot merge.
Then I do
$ git pull
Already up-to-date.
Try to do a git status
and check if you've got any non commited changes to 'file.php'. You need to commit all the changes on the same files, or git could change your non-commited file.
Try to make another commit after the pull, and then try to pull again, review any possible merge and push the data.
If you want just to overwrite your local copy, checkout the file file.php (git checkout HEAD^ file.php
to checked version previous to last one) to a previous version, and then pull from the repository.