When underground structures generate in the world, they should create empty space that should contain air. Instead, some other block that I can only assume is a placeholder fills the gap. Whatever block it is, it doesn't register as air with the /fill replace and /execute if/unless block commands.

The affected structures are:

• Caves*
• Ravines*
• Mineshafts
• Strongholds

*These are affected in both the overworld and the nether, although nether fortresses don't seem to be.

All other structures are unaffected, including caves and ravines that generate filled with water.