The bug
Although there are many instances of villages spawning over ravines, holes, ponds, etc ... this is the first where the village seems to spawn under the village.
I'm wondering if it found an odd hill generation and this is the result of interacting with it.
Seed and coords
Seed: -7437039540087077162
X: 1706 Y: 71 Z: 167
How to reproduce
Render Distance = 2 chunks
Use the following command: ⚠️ Make the terrain load earlier than the building.
/tp 1706 71 167
Use the creative mode to fly to the X: 1706 Y: 71 Z: 167.
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Is this still an issue in 19w11b?
This does still happen (buildings that stack on other building fill the lower building with sediment), but the seed no longer works since village building positions have been changed. I reproduced this using an AMPLIFIED world but this should also happen in default worlds occasionally. The seed and coordinates for this bug should be updated.
Confirmed for 19w13b. Use the seed 5006074542124220040 and teleport to -13642 72 2884 to see a destroyed village (no need to "load the terrain earlier than the building" or do any other actions in these reproduction steps).
Confirmed for 19w14a
This is still apparent in 1.14 Pre-Release 1, but it is way less extreme since villages were optimized so that buildings don't stack on top of each other. They instead just generate under overhangs and occasionally generate a bit too close to the stone, so this might be partially fixed.
Edit: apparently, it is actually fixed, which I can confirm after exploring many villages near hills.
I was coming to report this same issue. Multiple villages in the world I just made have houses that have been intersected by land, as if the air blocks inside the homes were not told to stay air blocks. The regular blocks will remain the same though.