For example, I had the Cursed Weapon quest for the temple, which incessantly spawns orcs to attack the player. I ran away from three such quest-created orcs and a bit later I found the NPC in the dungeon and delivered the weapon, which ended the quest. The orcs were still roaming the dungeon and I ran into them on my way back. They simply disappeared when defeated.
Similarly, there is a random quest from an add-on pack which summons a Giant in a town that the player is visiting, with the quest apparently ending when the giant is slain. The quest ending text implies that the player can loot the giant's body, but there is none left.
I'm not sure how this relates to vanilla DF behaviour though. Also I'm running a bunch of mods (list below), although I doubt this is caused by any of them: