It could be rebased upstream. While it's a really bad practice, it could happen.
As you say it's bad practice and shouldn't happen. I use gitlab and GitHub where branches can be protected to only allow merges via their web interfaces.
I'm not aware that GitHub offers the same functionality.
I am not well versed in working with git over ssh, but after following the instructions on GitLab to generate a key, then git would keep showing me the RSA finger print which doesn't match the one provided on the website. After looking around a bit, it looks like the one listed is ECDSA.
tl;dr: It was late. Finger prints didn't match. Only logical assumption was NSA. :P (Not really, obviously, but the finger prints could be more clear.)