If you take your house, and build the walls one tile in, they won't be able to do this to you anymore. So if you have, let's say a 10x10, but build the walls in like it's an 8x8 or 9x9, they can't hurt you anymore. It's a known house bug with customized houses. I've been killed on my crafter by nature's furys that somehow got cast up to the 4th floor of my house, but after fixing the wall it doesn't happen anymore. This was, of course, when I first got back into the game a while ago, and I didn't know what the heck was going on.