By virtue of liking a film, I wouldn't call it "bad," so I'll emphasize films I liked that ran counter to popular opinion.
I quite liked Batman v. Superman, especially in relation to the homogenous MCU factory. It was dark, epic, and felt like several movies in one. I wasn't crazy about some elements - the monster thing at the end was a bit one-dimensional and uninteresting. But overall it worked for me.
I also liked Dark Phoenix far more than the reviews. No, it wasn't Claremont/Byrne, but it was a lot better than the Radner fiasco. While I wouldn't call it a great movie by any means, the fact that it didn't totally butcher the Phoenix saga makes it pretty good. Sansa did better than I thought and some good performances throughout.
Here's an obscure one: Terence Malick's Knight of Cups. Yes, Malick is pretty pretentious, but he can also be quite deep and damn if he doesn't know cinematography. This is very much a "spiritual quest" story, and thus misunderstood by most of the viewing public, even the film snobs who were the only ones who probably saw it.