Alex's caves has a particularly deep ocean biome, so if a mineshaft spawns it ends up floating in the ocean rather than rooted to the structure. I'd probably blacklist that biome specifically for those mineshafts or place them far closer to the bottom of that biome at around -50.

It's an ocean mineshaft from Repurposed Structures mod
YUNG's Better Mineshafts mod doesn't have ocean variant