This is a bit of a late reply, but the reason it's committing everything that your colleague changed is that it's the definition of a merge commit. I find that

This is a bit of a late reply, but the reason it's committing everything that your colleague changed is that it's the definition of a merge commit. I find that it's desirable to avoid merges to reduce the number of overall commits. To do this, do git pull --rebase instead of just git pull when your commit is rejected.