I'm playing a world with seed 7704554005398968810 and a village was generated at location x: -675, z: -267 where all of the doors are two blocks above ground, preventing the people from going inside to survive the zombie siege.
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True. This is not even a glitch at all. All it is is just generation. Sometimes it derps, sometimes it's normal.
"It has always been broken" does not equal "working as intended".
It appears that the generator attempts to avoid this by filling in blocks under the buildings. I have seen them spawn above a huge chasm in the ground, and the chasm is partly filled in underneath the building so it is supported. It seems that the bug in this case is that the floor was generated as gravel rather than cobblestone, which immediately fell down into the water below.
Duplicate of MC-1948, please use the search function to see if your bug has already been submitted. Currently over 57% of tickets are being resolved as duplicate.
"Often in non-superflat worlds, villages will spawn unevenly, causing some houses to spawn too high for villagers to reach, or partially underground, trapping villagers who spawned inside."
This has been a standard mechanic of biome/village generation since 1.8 Beta.
There are various ways to deal with this when securing a village that are described on the Wiki.