Animals escaping in a completely fenced in area

In my single player, I have a sheep pen, below a pig pen, below a cow pen, below a chicken pen, which are all sealed off by fences, so there should be no way to escape. But somehow, the chicken's are walking up and down the staircase/in the cow and pig pen, there are cows in the chicken pen, there are sheep in the pig pen, and the pigs are the only ones staying put.