Found this bug while working on my dock with 4 rails, which releases 4 drones with logic.
The rack and all drones have faction modules. When I set my faction to the rack, you can see the the rack and all drone's indicators turn green, seemingly adopting my faction.
However, when I trigger the logic circuit to undock the drones, they become blue (neutral) while the rack maintains my faction setting.
Interestingly enough, if you manually individually set the faction to all the drones on the rack, their indicators remain blue and seemingly neutral (if you hadn't applied faction setting to the rack.) At that point if you undock them, they'll turn green again and have be part of your faction.