The bug

When saving witch hut structure data the game wrongly assumes all witch huts generate at the same height. As a result, witch huts generated higher than usual will allow regular mobs to spawn inside.

How to reproduce

Observe spawning in the witch hut at 8832, 9456 on seed "Witch hut test", pointed out by anomie x in the comments.

/tp @p 8832 100 9456

See attached screenshots: One showing three layers of witch spawning floors built in a witch hut generated at its usual height, one showing three layers built at the same height (relative to the witch hut) which generated above Y=100. One spawns witches, the other spawns all kinds of mobs.

Code analysis

Code analysis by Xcom6000 can be found in this comment.