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...
Stronghold 993 19 376
Skeleton Spawner -748 60 -914
Spawner: 7 28 954