So, I suppose my writing orbits around the science fiction and horror genres, so I'll be talking about them.
For Sci-Fi I do have one main gripe that I haven't seen brought up yet: ideology. While I don't necessarily have an issue with politics or ideology in stories (and in sci-fi it can be pretty hard not to insert that stuff anyway), what I do have an issue with is when the ideology or politics take precedent over the story. Often this causes the story itself to degrade in quality quickly as the author shoehorns things in to fit the 'message', and I have often noticed that frequently it seems the authors assume that they are preaching to the choir and characterizations are often loaded (e.g., in an eco-friendly story the villain is a hunter. That's it, they don't do anything particularly bad, but they are a hunter and that should be enough).
Also, black and white solutions to grey problems are a big buzzkill. Often, I find the stories I find to be 'deepest' are the ones that seem to be about nothing (i.e. It's Such a Beautiful Day by Don Hertzfeldt or Stalker by Andrei Tarkovsky)
For horror I suppose my peeves are fewer and less intense as I find myself recently falling out with an old love of science fiction and snuggling into a comfortable space in horror writing. But there are a few things.
Generally, I don't care for this either, with the exception of if the creature is tied or cleverly juxtaposed with a more grounded or human threat or problem. I think the two examples of this I can think of is Hell-Star Remina by Junji Ito (actually I like I lot of his work, though on the theme of more human threats The Bully is still my favorite) and House of Leaves by Mark Danielewski. The former dealing more so with the fallout of an apocalypse unfairly blamed on a girl and the latter a clever (IMO) metaphor for the distances in a failing marriage. Now ghosts are a thing I rarely can get behind, I have issues thinking of a time they've been done well...
The other thing is well, oddly enough, edginess. I used to be a creepy pasta fan, OG slenderman and all, but I think the edge arms race ruined it (Looking at you Jeff). Mindless, untargeted violence can be scary, but it can very quickly just be over the top cringe. There's an interesting observation by Slavoj Zizek (I think) in his book The Plague of Fantasies where he espouses an idea that there is no 'evil' just perversions. He gives the example of a case of an Austrian man held his daughter captive in his basement (even fathering a family with her) out of a perverse sense of fatherly protection. (source: https://www.independent.co.uk/news/world/europe/josef-fritzl-10-years-what-happened-daughter-dungeon-basement-incest-rape-austria-elisabeth-kampusch-a8322671.html)
Now that's horrifying. Like @smokesalty said, put some thought into the villain's motives, humans are scary stuff.