This is peculiar to MM9. Not infrequently, something will go wrong when you try and enter or leave a location, and almost always the answer is to return whence you came, save your position, exit the game, and delete the minisaves of the location you're having problems with. Then reload the game and continue, and the problems should have gone away. What you has happened is that a location has corrupted, and what you have done is to force the location to respawn with a new clean location.
I've used it to restore a corrupt location, and to restore one of the the teachers when he or she has gone missing.