Minecraft – In Minecraft why do mobs get stuck in the ground

Given the square nature of the missing pieces, I think it's some kind of Chunk error ("chunk" being the term for any given sector in the minecraft world).

Specifically, from the notes about patch 1.2_01 on Notch's blog, emphasis mine:

• Added a temporary fix to get rid of chunk visibility errors

The last one is interesting.. The problem with chunk visibility errors was that for some reason the “dirty” flag on chunks and the list of “dirty chunks” got out of synch. There wasn’t time to try to do a proper fix today, so I just made the client check a couple of dirty chunks per frame to make sure they’re in the list.

So until we fix it proper, you might get invisible chunks, but they will fix themselves after a second or two, usually way before you even get close to them.

There are two points to remember that may seem contradictory: first, like Nicholas pointed out, you need to makes sure that your mobspawner is the only nonlit space in a pretty big area around you (I think the area's actually about 150x150 blocks), but second, you need a lot of empty space around. In other words, minecraft will choose places that have a lot of surface area (not volume) to spawn mobs in, so if you were to have a lot of open caves beneath your mobspawner, the game will flag that area as more likely to spawn mobs in. You just also have to make sure that it's all well-lit, then you've effectively tricked the game into flagging that area to spawn mobs in, but then conveniently your mobspawner is the only dark area where it can do so.

I would recommend you take a look at this tutorial. You may not want that particular style of mobspawner, but it goes over the prerequisites of any good mobspawner quite nicely.