Aliens was ruined for me when Ripley incorrectly brandished a marine-issue Armat M41A Pulse Rifle in a tropical M-class atmospheric environment. Destroyed my illusion of realism, that did.
There's a knuckle-bitingly bad deleted scene from the 2009 Star Trek that is notable for two reasons:
1 - it was fully shot, soundmixed, edited, and SFX were added, so at no point did anyone think there was a problem with it until after post production, and
2 - it is notably hard to find online compared to other deleted scenes, almost as if Paramount made a point of deleting videos of it from the web, but not other scenes from the same film.
It was available on the first blu-ray of the movie, though: in the scene, the green lady Kirk was sexing earlier in the movie was killed along with everyone else on the Saratoga, and afterwards he sees a green lady in the corridor of the Enterprise and starts talking to her as if she was the green lady that's dead. So basically, the writers and director of Trek saw no problems with a scene where Kirk can't tell people apart if they're a different colour, but when you start thinking about what this says about how Kirk as a character views women, it just becomes more and more disturbing.