In order for drone recall to work properly the mothership must be the flagship the fleet of drones you want to be able to recal. However, while messing around with fleet mechanics, I have discovered that recalling drones to a mothership that is not in a fleet offers mixed results. The drone fleet's flagship will not respond to commands, but other ships in the fleet will return to carrier with varying degrees of success.
This can also be duplicated using a mothership that is in a fleet, but not the flagship.
Not incredibly important, but this appears to be a bug nonetheless.