Sometimes NPCs can be defeated in quest instances. Many even fail the quest if this happens.

As for the case in point, it's possible he chased an enemy far enough for the game to decide he needed to go back to a "home point" of sorts. It's also possible some other event just triggered the quest instance to say he needed to be at a certain point right then and forced him to do so.

If all else fails, simply repeatedly trying main and class quest instances gives you buffs on the third and later runs to make it easier if need be.