There are a few quests where you can complete an objective before the objective becomes an objective, thus rendering a quest uncompletable due to it not counting. Thralls of the Fungus Lord destroying the mushrooms in the end room before it tells you to, The Spawn of Whisperdoom killer her with range before the game tells you to, etc.
Those two have caught me a few times before, so they are the first ones I think about.
Oh, Frame Work as well, if you use a ballista to get in and you land right beside the gate, you can get inside to assassinate the chief before that objective comes up, breaking that one too!
BEWARE!!!! *makes eerie noises whilst wiggling fingers ominously*