There are a couple big turn offs for me in sci-fi.
1) Incorporation of psuedo-spiritual bullshit. This is science fiction, not fantasy. And a big no-no here is trying to scientifically explain/encorporate real-world religious (Seen waaaaay to many "Egyptian gods are really aliens" movies out there) It has yet to be done in a way I felt satisfied with, though Stargate held my intereste because the religious aspect was all a scam on the aliens behalf. This aspect was the sole point of contention I had with the otherwise very fun "5th Element". Incorporating magical or similar elements tend not to work well either. Star Wars lost it's spot as the sole exception because it fell into exactly what makes it fail. In "A New Hope" through "Return of the Jedi" it worked because it, like religion in the realworld (if you are a believer) was beyond explanation and could have profound, if subtle, impacts with only the occational overtly obvious "miraculous" moments. Hell, even one of Vader's admirals doesnt believe it exists till Vador shows him better. I actually considered Star Wars to be a blend of Sci-fi and Fantasy...until Episode 1...and the miticlorines (sp?)...
2) Why the hell is it humans and aliens always seem to be able to interbreed together? At least Star Trek had the whole thing about all the races being seeded from a common ancestral races...even that is really flimsy if you know biology well, but I could accept that because, as GOOD Sci-Fi should be, it was fact taken just a little further.
3) When either humans or a specific alien race is universally, scenery-chewingly evil...really, it is like a projection of the writters own racist tendencies filtered through a veiled medium. I found it laughable how another poster on the forum referred to District 9s aliens as "heroes," as I actually found that movie to be an excellent blend. There were a lot of asshole humans, a fair share of decent ones, and the same could be said for the Prawns. I watched this with my fiancee and she and her sis chewed the humans for opening fire on the aliens and I couldnt help but ask if they missed the fact that one of the humans was disembowled by the alien they shot not 4 seconds before they opened fire? It was a fair depiction of a tense situation with frustration and fear on both sides. The only true hero of the story was Christopher in my Lofty-Standards-Of-Good eyes and his son gets high marks as well.
4) Black holes...we know enough about them that sci-fi's fav plot tools and elements with then are all realized to be incorrect. there are still lots of creative ways to use them in a story, but sci-fi seems hung up on using them for time travel and wormholes.
5) Why are aliens almost always more advanced than humans? One of the most charming elements of my favorite sci-fi of all time, the "Alien" trilogy, was that it was debateable. They didnt know squat about technology, but they could definetly outcompete the race who's ship they found in the first movie. And if it werent for Ripley I would dare say they got the human race beat there too.
6) Unlikeable female characters...though this miff is actually a general gripe as of late. And before the cries of sexism pop up I would first pose this: Is it possible for a female character to be feminine without it being her sole niche, capable without just cloning the capable male hero and giving it a gender swap, not a total ***** to every male she comes across (asshole doesnt translate to sexy or cool), and not unneccesarily sexualized? I argue yes. Yes and why has noone done this since my beloved "Alien" trillogy. Ripley goes from basically garbage collector to survivor to hero all while still being a woman...not just in the collection of parts, but in her personality and behavior. She goes back for the freaking cat of all things! Moreover she displayed excellent motherly instincts with Newt, showing down with the big baddie at the end all while still showing a realistic level of terror despite the absolute bad-assness of it all. "Alien" and "Aliens" are still my go to movies to prove that a woman can be an awesome hero without just being a dick-less man with tits.