In Dripstone Caves and also Lush Caves, the features that go down from the ceiling and sometimes the floor too (Stalagtites, Glow Berries, Stalagmites) will carve into their terrain to generate, even Mineshaft floors!
I also found an instance where this occurred underwater and technically created air blocks
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We're tracking this issue in MC-221311, so this ticket is being resolved and linked as a duplicate.
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The mineshaft issue is currently being tracked on MC-221311, but it seems like mineshafts are not the only place with this issue, I saw a bug where glow berries generate 1 block too high and penetrated the roof of a cave