Upon logging off and logging back in an Survival Mode World. If an passive animal were to be near a wall, it would die of suffocation. (Edit) Also when loading a pre-loaded chunk as well.
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The only solution i could find is when you block the wall with fences. I've also tested it with glass, and they seem to be ok. Either way, it's an annoying bug.
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Confirmed to work on the server I play on.
They actually fixed this a couple versions ago and now it's come back. Kind of sad to see the animals I try to breed dead on the ground as meat and leather.
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I think what is happening is the animals are pushing each other into the walls. I've seen this happen with breeding as well.
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I had a small pen of chickens at my SP snapshot base. Today i went from 13w03a to 13w06a. At the start there were several dozen chickens in the pen. I spent a while mining directly underneath the base and came back to only a few chickens left alive. The remaining ones would walk into the dirt wall and quickly die. This continued until all the chickens were dead. There was nothing else to push them into the walls.
In my case it did not seem to have anything to do with logging or chunk loading. I haven't noticed dramatic fatalities in similarly constructed pig and sheep pens nearby.
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I have also seen this with villagers.
Confirmed. Happens on my SMP server a lot in certain pens, though strangely not in others.