Breunor

Having this issue with 13w07a as well, doesn't matter if the water is flowing or a static source block. Hatching a chicken into water causes it to drown.

Using 13w07a, this happens to animals and villagers non-stop. Usually due to having multiple animals/villagers bumping each other, they eventually ignore blocks and enter them. If glass they will go all the way in or even pass through (and can then run around my base until caught), if anything other than glass they quickly suffocate and die.

When standing on a slab, even when alone, very easy for say a chicken to fall through the slab and remain there, without bumping into another mob to cause it.