Livestock sometimes vanish when areas are reloaded/unloaded. I have experienced this with sheep (dyed and undyed) in a 6x9 enclosure. These sheep are fed and sheared multiple times, and potentially bred as well.

We have additionally seen this with horses on the realms server. The horses are tied up with a lead and in two instances armored. When returning/reloading the area, the lead can be seen tied to the post with no horse attached to it. One instance during a server crash resulted in a ridden horse despawning.