This used to be Revenge of the Sith for me. It still kinda falls into that camp but it has a lot of issues and I totally see why people feel the way they do about it. I feel similarly about Batman vs. Superman and Star Trek: Into Darkness.
Others....hm, I thought Chappie was solid. I actually think the first The Amazing Spider-Man movie is pretty great, whereas the second one falls into the aforementioned "great but full of issues and I totally get peoples' problems with them," category. Spider-Man 3 used to be this for me but the last time I watched it I realized it was totally mediocre (though still not really much worse than 1 and 2 which I don't think are that great now). Avatar definitely, people these days underrate how much of a visually stunning and well-directed that movie is. American Ultra is pretty good, I don't think the reception was that bad but I thought it was pretty damn underrated.
Prometheus was....fine. Like I wouldn't but it into the top category if only because I don't think it was totally flawed, but while I don't think it was great, I enjoyed watching it and I don't really get the hate at all.
Probably a bunch of random comedies I grew up with are also this. "Daddy Day Care," is still memorable to me for some reason.
Dark Knight Rises and Interstellar aren't really unpopular movies, they just have a vocal hatedom I feel like. For what it's worth I think both movies are fine but also proof of why Nolan isn't some sort of directorial god people think he is. Star Trek Beyond definitely isn't this, most people seem to like that one, it's just that it didn't do super well at the box office iirc.