Well, the thing to keep in mind is that "science" doesn't just mean facts and rules, it refers to the process we use to investigate the universe and distinguish valid ideas from invalid ones. So the way I read the question is, what SF movie was most disrespectful to the process of science or most badly misrepresented what science is?
One film that's always deeply annoyed me in that regard is Flatliners. This is a movie about a bunch of med students who are conducting an illicit "experiment" where they basically induce clinical death in one another for a few minutes, then revive each other and document their memories of the event as "evidence" of near-death experiences and/or the afterlife. Okay, it's sort of a supernatural thriller rather than strictly SF, but still, it purports to depict what the characters are doing as a scientific exploration, and nothing could be further from the truth. Science depends on repeatability. An experiment serves no purpose unless its results can be independently replicated and verified. What these students were doing relied entirely on subjective, unrepeatable, anecdotal accounts. There was no way they could possibly be verified, so they weren't scientific evidence of anything. The characters claimed that because they had experiences while their EEGs showed no brain activity, that was "proof" that they'd experienced something other than a hallucination or dream, something that happened to their consciousnesses outside of their brains/bodies, but that doesn't follow, because their minds could've experienced all those events in the brief moments before or after their brains shut down (since purely subjective, mental experiences can seem to take much more or less time than objectively elapses) or they could've constructed the memories after the fact to fill in the gap in their perception. Without external verification, there's no way to assess the reality of any of it. So there was nothing at all scientific about their methodology. They were just risking each other's lives for no reason. And that's what makes Flatliners one of the most insultingly wrong depictions of science as a process, even aside from the fantasy elements of the story.
Of course, there are countless movies, generally horror films and the like, that insult science by depicting it as dangerous hubris, tampering in Things Man Was Not Meant to Know and paying a karmic price, or as a cold, heartless discipline that's morally inferior to just going with your feelings or whatever. B-movies in the '50s were full of this. So in this case I'd rather cite an exception, a rare movie that treats science respectfully. That movie is the original The Fly. You'd think it would be a classic anti-science parable whose point was that David Hedison's character was wrong to try to "play God" and got the punishment he deserved for his arrogance. Instead, he's portrayed more as a tragic hero who chose to take a risk for the worthy cause of expanding human knowledge and should be honored for his sacrifice.