My FanFiction Pet-Peeves:
#1: Authors who post chapters based on reviews.
Most of the time, authors will post one or two (three if you're lucky) chapters at a time, and then won't post another one until they get a certain number of reviews. Some go even further and say that, for example, flames don't count toward this total. Some set their quotas outrageously high. Who would want to click the button 100 times just for one new chapter!? Seriously.
#2: Authors who don't check their spelling or grammar.
We can't read stories that use poor grammar. The occasional 1337 werd for comic effect is OK, but please try to AT LEAST use proper punctuation and capitalization.
#3: Un-necessary messages on story summaries.
"R&R." "I suck at summaries." "My first fic." "T for safety." Do any of those seem familiar? Ten bucks says you've seen, if not actually used, at least one of 'em. They take up a whole sentence in the story summary, which can only contain 255 characters. That's as long as a Windows long file name. While that's good enough for most purposes, these unnecessary messages take up valuable summary space and should be left out entirely, or at least put somewhere else.
#4: Formatting issues.
Sometimes whole chapters will be bolded for no reason, making the thing extremely hard to read. Now this isn't necessarily the author's fault (it could be a Document Manager bug, for example), but it's a pain in the gluteus maximus to read them.
#5: Disclaimers in every chapter.
Now I understand it's important to acknowledge the "gray-zone" status of fan fiction (and some people can get really creative with this), but including a disclaimer on every single chapter is unnecessary and repetitive. One disclaimer in the first chapter (or even in the summary, if it'll fit) is enough.
#6: Random author's notes in the middle of the story.
Those with egos will sometimes interject random author's notes into the middle of the story. (A/N: For example.) Now, I do not discourage author's notes, but they are better placed at the top or bottom of a chapter, preferably set off from the story text in some way (e.g. bolding, or a HR). Putting them in the middle of the chapter detracts from the story.
#7: Excessive language, drugs, violence, and other content.
Seriously, people actually find that stuff FUNNY!? What losers. These are the same people who laugh at the word sextillion, which if you're like me, you know it means 10 to the 21st power (on the American scale) or 10 to the 36th (on the European scale).
#8: Pairings.
There is no need to announce a character pairing in the summary. It's dissappointing that there are readers out there who care about nothing other than character pairings. But meh.
#9: Songfics.
Most of them are songs I've never heard of, and most of the time they're way to short.
#10: Authors who give up on a great story.
Too many people have started up great stories, with great, original ideas, and then halfway through they decide they can't write anymore for whatever reason (they're working on a crossover, nobody's reading it, etc.) -- They might have even intended to finish it, but nobody's perfect -- and they just abandon it. I've seen stories from 2007 and earlier still labeled "In-Progress".