Just before the emperor in the volcano series of quests, two party members cast Spirit Guardians, and one used Dust of Disappearance.
The dialog went as normal, but afterward, the emperor never started the fight and we killed him and the wraiths just by standing next to them (the Spirit Guardians were doing the damage).
Got the key, no problem. Quest updated.
Still invisible and Spirit Guardian'd up, we had the dialog with Urka. Killed him and the soraks the same way - stay near them and let the Spirit Guardians kill them.
But... the Urka quest never updated, even after looting his stuff. That breaks the quest line.
There are several more places this happens. The only one I remember was in the final quest, when you are attacked by fire spiders and fire elementals, the platform doesn't move if you stealth kill them.