I've noticed sometimes when I invade planets and I win by a large margin that I get one of my troop transports back, but the population still remains on the planet. For example, I just attacked a world with 2 transports and 2000M troops. I won the battle with 1700 troops (using Info Warfare). After the battle the planet had 1700M population, but I still had one of the troop transports with 1000M troops in orbit. Seems like the bug is that the planet should only have 700M population -- the 1000M people are not being deducted after being put back into the Troop Transport.