Just when the fandom takes a character and gives them some strange character development. Like the whole Derpy and muffins thing, or Pinkamena, or Lyra is obsessed with humans, or Time Turner = Doctor Whooves. (This means a lot, because I LOVE Doctor Who.) It's for this reason that my support for the Rarilane ship has crashed.
I also don't like the fanmade music very much. I used to love it, but now... Eh.
Fancomics or fanfictions that have the ponies cursing all the time or have a mature rating. If you want your fanfiction to be in-character, no cursing and no mature content!
That being said, sexual themes as far as fanart and fanfiction goes. I'm not against furries, but I try to avoid mature fanart when I can.
Fausticorn. She's cool and all, but she makes no sense in the canon.
Trixie, Lightning Dust, Gilda, Trenderhoof, etc. They were not cool characters. I don't know why everypony likes them.