The Bug
The air blocks in the amethyst geode are

minecraft:air

instead of

minecraft:cave_air

.

How to Confirm

1. Find an amethyst geode.
2. Stand in the center of the geode.
3. Run the following command.

   /fill ~-5 ~-5 ~-5 ~5 ~5 ~5 minecraft:glass replace minecraft:cave_air
   

What I Expected
The air in it should be replaced by the given block (in the sample is glass). However, no air blocks in it were filled as in other generated structures.