ok so I checked around and didn't see this bug.... if you stack transports together and conquer a planet the remaining number of people stay on the planet and in the transport. If you attacked with say 5 grouped transports with 5000 troops and lost 900 troops, the planet will have a population of 4.1 billion and you will have 4 full transports left over. This is normal 1000 troop transports. The bug changes to use up the least amount of transports vs. invaders vs. capacity. So if you had 3 stacked 3000 troop transports and won with 5000 troops remaining you would have a population on the planet of 5 billion and one full transport remaining. Talk about war-babies!