I had noticed that most of my animals have been able to get out of their pens, I had a suspicion that it might have something to do with either the hitbox of the grass path I used in front of my gates, or that it was an issue with entities' collisions when a world loads in.

To test this, I gathered up my animals again, saved screenshot A and then proceeded to save and exit the world, when I returned, the result is screenshot B, some animals had been able to clip through the fence blocks.

I did a quick search on the bug-tracker, but I did not find any issue for the current snapshots, so if I missed one, I'm sorry.