In the latest Snapshot, Tamed Rabbits will seemingly Despawn when ever you put them in a Fenced off area. I say seemingly, because I think they actually turn invisible.

What happened was that I had placed a Tamed Rabbit and a Baby Rabbit in a relatively small fenced spot, and went to go fix something a Creeper broke. When I went back to check on my Rabbits, both had seemingly despawned. I promptly removed the Fences, and went to my Carrot farm. Shortly after, I noticed my Carrots started to get uprooted, like something was jumping on them, but the dirt itself stayed Tilled. I left the world, and loaded it back in, and the carrots were still being uprooted.