For published fiction, my current pet peeve is the Girl Who Hates Femininity. She hates makeup, but she's naturally gorgeous, and she thinks cheerleading is stupid (as opposed to a physically exacting competitive sport; I'm not a cheerleader, but there is no way the things they do don't take effort and practice), and she wouldn't be caught dead in a skirt, and she thinks the popular girls are stupid, and she couldn't care less about boys and anyone who thinks otherwise is stupid. Thinking someone else is "stupid"/"wrong" for thinking differently than you do isn't okay, regardless of what they think.
For fanfiction, I'm annoyed at the people who think that they should tag their story with the pairing of X/Y when the only mention of the pairing that X is Y's ex-girlfriend from years ago, and she was a horrible person, and the story's all about Y/Z. If I wanted Y/Z, I'd be looking for it in its section. At the very least, make it clear from the summary that X/Y isn't the main pairing.