They STILL haven't fixed cobblestone walls in relation to the AI. The AI defaults to thinking they are regular blocks, so mobs will wall hump. You wouldn't notice this much with penning regular mobs, but mobs that try to specifically path get forgeted. This is most noticeable with villagers, where they try to path DIRECTLY to a door and won't diverge from the path. If a cobblestone wall is in the way, they are forgeted, trapped there until the zombies get them because they don't think to go the forget around.
I tweeted Dinnerbone about this - hopefully he'll do something about it... Maybe I should tweet Jeb too, but Dinnerbone is the one active at the moment.