I found a skeleton spawner. I placed torches on the four sides plus the top side; the room was small enough that no skeletons should have been able to spawn. Then the skeletons started to spawn in the floor and the walls.

Right now the spawner seems to only spawn them in a block on the west side and the floor.

My guess is the spawner is not checking that the skeleton is clipping into blocks when it tries to spawn them.