I do not know the exact cause, but i have unobtainable keys and am unable to unlock hive mind. I have completed around 10 runs, unlocked all character quests (except the last comrad one). Multiple floors (all t3s and core)  list 0/1  keys, but they never drop when i visit them.  

I think this was caused by acquiring multiple keys in multiplayer and turning them in at the same time. I have seen and picked up keys on every floor, but some of them seem to have not counted toward meta progression but no longer drop.

No reproduction steps, the last run i did where i got keys was a friend hosting to get me through (locked) vault and hive mind, which both dropped keys but only unlocked vault.