This might sound like an odd thing to do, however while one can upgrade colony ships to becoming military transports without issue as they have population on-board, it's also possible to ships without population, ex. scouts, to military transports. However, as these ships have no population, they become military transports with 0 population without a means to shove troops onto them. I'm not sure if there's either a way to allow players to add more people to colony/transport ships, or disallow ships without population to be upgraded to colony/transport ships, though something should probably be done about this.