Painfully stupid characters who are painted as your "average" person. You know what else? This:
"Oh hey main character, I'm in love with you. Um, you don't have to tell me what you think, umm..." A real man would give her a response, right? That's the respectable thing to do after she mustered the courage to tell you. But not our hero, oh no.
"K that's nice." ...then 50 episodes later something pivotal happens and he's like "OH YEAH there was that one time she told me she liked me. I conveniently forgot, oh yeah." burning_eyes
Filler episodes....dear god how i hate filler episodes. Though some of them can be good, i just wish they would get on with the ACTUAL story. This is why im starting to lose interest in Bleach (the english dubbed ones), JUST GET ON WITH THE ARANCAR ARC ALREADY classified_fu
I can't think of anything specific to anime/manga. Horribly written characters and cliched stories can be found in any media, and they don't always apply to anime/manga. Hell, I'm going to be naive hopeful girl and say that most of the time they don't.
But I will say that anime fans annoy and terrify me more than any other kind of fan. So yeah, I'd say the fans are what I hate about anime. The obnoxious and/or crazy ones, anyway.
When series you enjoy isn't overly unknown therefore it's barely updated online.
When your favorite has a mostly creepy male fan base (Sometimes, it's hard to be a Touhou Project Fan Girl).
Fan Girls. Yaoi Fan Girls.
Series that become overly huge like Naruto/Hetalia/Whatever is more popular then it should be. Fans that post pornographic fan art and fan fictions.
The stereotype that anime fans are always inside on the computer, unsociable, unattractive, pasty skinned virgins that go "Kawaii Nano Desu~! <3" all the time and whatever else is to that stereotype.
The anime fans that add to that stereotype.