I managed to catch this while going around underground in spectator mode.
A geode spawning in the same place as a mineshaft causes the blocks next to the mineshaft to be replaced with air. This was right underneath a taiga, hence the ferns growing on top of the dirt.
Seed is 9163275066495055902, the coordinates are 1511, 42, 22
At least the bats seem to be enjoying it.
[media]Related issues
is duplicated by
Attachments
Comments


Please provide the seed and coordinates.

X: 1511 Y: 42 Z: 22
Seed: 9163275066495055902
I'll add it in the main post as well.

The generation seems to be dependent on which direction you approach the geode from when the chunks are generated. For the seed in this report (9163275066495055902), approaching the geode from the south has the geode take priority over the mineshaft, instead of the mineshaft taking priority over the geode.
Switch to spectator mode.
Teleport to 200 blocks south of the geode:
/tp @s 1512 43 211 180 0
Fly straight (north) for 200 blocks.
The geode looks like this:
[media]
Edit: This is likely MC-55596.
Can confirm in 20w51a.
Can confirm in 21w03a.
Can confirm in 21w05a.
This issue can no longer be seen in 21w06a using the provided seed + coordinates.

I found this in 21w06a but different, the logs that now come with the mineshaft goes through the geode
seed -2214449187411849531
coordinates -150 -15 660
[media]
In such case, minecarts with chest may embed in calcite. The rail block is gone but the minecart vehicle has not been replaced removed.

This is the intended order of world gen operations. The geode generated before the mineshaft, which then tore through it. The reason there is so much open air there is because of the mineshaft room that is generated there.

I hope this resolution will be revisited one day since contrary to the previous comment the geode does not always generate before the mineshaft, it depends on the order in which chunks are loaded.