I think it's because they're trying to run away from something and the doors are blocking them, so they try to bash it. I usually use Animal Empathy on them and then release them to get them to stop, but yeah... the squirrels have been behaving like this pretty much from the time they were added to Degannwy. I figured it's because some of Degannwy's denizens don't have animal empathy, causing the squirrels to go hostile and try to run away like animals do in the wilderness, which then triggers anything they run by to start buffing and it is pretty immersion-breaking. Blue's probably right though, more than likely it's just a question of adding the squirrels to Degannwy's faction.