Another one that I mostly see in fanfic, but I've seen it in discussions for books too.
Folks, everyone has their favorite pairing. Some people even have their OTP. (One True Pairing.) And MY favorite pairing is just as valid as YOUR favorite pairing, and vice versa. (Even if one is slash. Different strokes and all that.) So can we please not get into shouting matches over how the fans of pairing X are all terrible people who clearly never read the book/watched the movie/whatever? There's room here for all of us.
(Yeesh. I love Avengers fanfic, but some days I want to smack the entire fandom. Happens in Dresden and Harry Potter, too.)
It happens in every fandom. Every. Fandom. Always. The latest review I got on one of my fics was someone yelling about how dare the rest of us not only write canon pairings. She included one in her list that was completely disproven
in the show.

Fanfic Specific:
1) Yes, please mark AUs. If not for the people who don't want to read them, then for the people like me who do. I've seen at least four fics that, by the summary, I wanted nothing to do with, until someone mentioned they were AUs.
2) I actually don't have a problem with people making siblings and such for characters we don't have this knowledge for (if we've met A's only sibling, don't make more, but if we know nothing about B's family...). I just don't want to see them as major characters. If I want to read about your characters, then publish an Original Story and I'll buy it. Keep it out of my fandom.
3) Please, by the love of all that's wonderful, mark your fluffing slash/femslash! Preferably with what couple it is! This isn't even a pet peeve, it's just basic ettiquette!
Overall Writing:
1) Poor spelling/grammar/word choice. Just. No.
2) Some basic research at least! I swear, I do more research for the daily writing challenges than some people do for their novels!
Okay, this example isn't from a book, but it makes my point. Character in a show is talking about his youth, namely his time in the US military. Apparently this enlisted man, at 18, was a Lieutenant in the Air Force, being allowed to fly jets, and receiving no real punishment for actions such as crashing said jet, nearly killing people in the process, and getting into bar brawls weekly. For some reason no one could understand why this ruined the episode for me (child of two AF vets), and why 'his commanding officer liked him' wasn't an excuse.
There is no excuse for something like this. It didn't just kill the episode, it killed the
character for me.