A few other people have encountered problems with NPC locations, though not this severe.
In general, if NPCs shift locations (possibly caused by alt-tabbing out of the game and back) it is only slightly, so they would have to be standing right next to a wall to have a chance of getting stuck in it or moving through it.
Some people have had one or all of the BF merchants shift location each time they entered the BF, causing them to become unavailable if they moved into a tent, etc, though eventually they would just come out the other side. There is a way to reset NPC locations, described in the topic below.
Teleporting anywhere (via hex editor)I'm not sure if there is anything that can be done to prevent this. Usually when there is a problem it is a one time glitch, and an NPC-specific fix or workaround is fine...
Creatures in the BF can sometimes be placed in areas you can not get to (though I don't see that happening 30 times on one level), and there were a couple maps changed in the main game during development that stranded a few monsters outside the normal play area.