Sometimes when I visit a town I find there are no guards at the gates and all the buildings are deserted. I have seen from time to time a bug where the character models are not drawn, both your own and NPCs but a quick save and load cycle usually fixes this. You can see if that has happened as you can still mouse over an NPC and get the speech bubble to appear even though you can't see them.
This is something different however. If the town got wiped out no one had swept in to take over, which would have been a nice thing to see. Maybe even hanging a sign over the entrance stating "Under new management".
