When villages and caves spawn together, bad things happen. Sometimes the villages generate large amounts of land right over the ravines and caves, which solves the issue, however this is not always the case. This prevents villagers from getting to various buildings, and it just looks bad in general. This also allows zombies to spawn in caves, then walk out and pursue villagers.

To reproduce, simply go from village to village until you see that a cave or ravine has destroyed part of a village.

Possible solutions include:

Having all villages create their own terrain in the face of unfriendly natural terrain, as some already do.

Prevent caves and ravines from surfacing near villages.

Prevent villages from spawning on surfaced caves and ravines