When the author doesn't stay true to the universe the fanfiction is written in.
It really pisses me off when they go away from the canon. I get that it's fanfiction and they can manipulate storylines/characters a little, but not to the point where the whole system is ruined.
E.g. A long time ago I read a Harry Potter fanfic where the reader thought it went up to 8th year, not 7th. Holy crap.