Since all indoors locations are in essence instanced like a dungeon in a MMO, perhaps it would simply be easiest if each quest had its own pre-generated location complete with all of the monsters, characters and items the player needs to complete that quest.
That way you simply COULDN'T muck anything up by going into that dungeon while just exploring or doing another mission...except if you have two quests in your log at the same time that both point to that same location of course... Darn!
That way you simply COULDN'T muck anything up by going into that dungeon while just exploring or doing another mission...except if you have two quests in your log at the same time that both point to that same location of course... Darn!