Air pockets connecting corridors to the central (dirt) room of abandoned mineshafts and gold mines are spawned at the wrong y-axis (above and below, respectively). In some extreme cases, this can result in any tunnels being completely seperated from the central room by blocks.
When spawned in water bodies they will not update, allowing the player to easily locate them. Seeds showing this occurence are provided in the comment section.
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They can occur in any seed. The images shown are using my test seed 'shroomzy' at different locations. I have yet to find a seed generating them near enough to the spawn to show it as an example.
I couldn't reproduce this with the seed given above.
If this still affects 0.16.0, could you please add seeds and coordinates of the places it affects (use /tp @p ~ ~ ~
to get coords)