I have to say that the mob AI (I assume that animals basically use the same AI as enemies) can be really annoying at times.
You put animals in pens, and they just stand at the wall jumping up and down. It would seem that they decide on a place they want to go, and they are going to try and get there if it's the last thing that they ever do. I've set up 4 different pens (chickens, sheep, cows and pigs), and I have auto breeders and chronotypers pulling out the babies. The babies are placed on a conveyor which takes them to a smaller pen, where once they're adults, they are auto killed by a grinder. The number of babies on the conveyor at any time because they're trying to run against it, means that they sometimes mature before they get to the pen.
Another time I snagged a Pec so that I had an easy way of trading with him, but if I left him in a pen with walls, he'd just jump up and down at one.
On a side note (I don't know if this is Thaumcraft or Vanilla MC), I've got a harvest golem for my mana beans, I built two walls with beans on both sides and the two golems are based in between. When they try and get around to the other side, they get stuck on the pods, and are therefore unable to reach their target. I swear sometimes it's like Daleks and stairs.