I had already 7b in port i had only millions when i first discover the bug. I sent all my drobe to the pirt then i accidentally cleck the create button on battle factory. The bugs here is the drone. Drone bay is useless...
I've tested as much as I can and cannot reproduce what you described, it only lets me build the amount of drones I can hold. The negative number it gives in the Ship Factory signifies how many drones you need to station somewhere in order to build more. It won't allow players to build more than they can hold at once without making room.
Are you able to reproduce this?