Falling sand or gravel overwrites some blocks when world generates.

When caves or structures generate in the world, sand or gravel that is exposed erases the block(s) they land on.

Bug causes the over-writing of blocks, namely: spawners / chests / end portal frames / moss stone / mossy stone bricks / cracked stone bricks / stone bricks / etc...

Seed: -1082223639696259069
Stronghold 993 19 376
Skeleton Spawner -748 60 -914

Seed: 8632520611045298466
Spawner: 7 28 954