I've only ever had this happen when using an unbreaking-enchanted pickaxe in multiplayer. So I assume (as others have said) that it's related to these two things.
I don't think that the burden is really on Mojang for glitches involving texture packs. While I do think they should (and probably will) address TP issues, it's hard to call third-party content problems a bug. And since the latest snapshots introduced changes to the way textures work, this might have altered the way low-res TPs should be made.
@PokeCanada: I've seen a 2x2 texture pack that worked perfectly. Enough said.
Mobs (not just the farm animals) glitch through everything: fences, walls, slabs, full blocks. This issue has seriously been around forever, so I doubt it will ever be fixed.