I found two weird squares that are filled with air and one layer of dirt close to mineshafts. One was above y=0 and the other one below. It seems as though the tunnels lead into these "rooms" and they generate according to the biome above.
Environment
The seed is: 6920284681567255947
Java version 8 update 271 (build 1.8.0_271-b09)
Intended. These rooms have always been part of mineshafts.