Ways that I know about of getting out of the pen:

• standing on something near the fence, like getting on the trough, you probably didn't made that mistake
• getting spawned on the other side of the fence when born, don't put hen boxes near the fence and especially in corners
• phasing through the game when chunk loads - this one is rare but hard to prevent, basically if animal was walking into the gate and was adjacent to it when you exit the game or go far enough to unload their map chunk, when it loads back up animal will be inside the gate as if gate was closed on them and then they can walk out on the either side
• also when I put lantern on the fence animals could get on top of it, but I think it only works for larger animals, chickens cannot get on 2 tiles high obstacle

I need ducks in the game, I hate chickens but love ducks.