Docking Modules have been updated. The carrier will not erase the list of docked ships on carrier undock/connection and base enter anymore.
It does mean ghost ships in docking bays have returned, but it should be at a way smaller extent than there used to be. I'll wrap my head around a permanent solution to fix this bug (and implement the carrier update) once Cloak Disruptors, Hyperdrive Disruptors and Hyperspace Beacons have been implemented.