Small livestock like chickens and hares are often raised in small cages, but in game they can't stay inside because of their too big collision boxes. Instead, they teleport frequently to the upper level 
For example, on this unfinished chicken coop (image & blueprint below) I have created 10 nest boxes. I can place chickens on the upper level just under the roof, but not on the lower one, even though they look big enough.
