The two biggest anti-features for me are the star system and the contribution activity green tile thing that appears on a user's page. To me personally, both of these systems subtly frame one's commit frequency and stars as a measure of how good they are as a programmer.

I believe these "features" turn the site into a pseudo-social media outlet and allow vanity to creep into process by which communities develop software. It is something that I noticed quite a lot during my (recent) years in undergrad: where many individuals directly equated stars with software quality (in there own projects or the projects of others). I know that those features in particular are only part of the problem (if the problem does truly exist), but they personally made me uncomfortable with the platform and are one of the primary reasons I left GitHub a few years ago.

That's just my opinion though, so take it with a grain of salt.