To reproduce:

Create a new world with the seed: 93921311

Go into spectator mode

/tp 140 45 170

Observe how there are small sections of a mineshaft, completely unconnected to each other. The mineshaft is clearly missing sections where the aquifer is generating.

It seems like the mineshaft just doesn't generate sections if there's an aquifer where it tries to go, but does generate sections on the other side of the aquifer.

See attachments for the kind of generation this creates