In cave worlds, structures are spawning above and at the bedrock level. I found the bug in a plains generated cave world, but others have found the same bug in other biomes as well.
Villages, Nether portal ruins, Outposts, and Ponds are all spawning at bedrock level (the flooring is also replacing bedrock, leaving mineable blocks to escape to above bedrock.)
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We're tracking this issue in MC-129235, so this ticket is being resolved and linked as a duplicate.
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