Hmm...I'm having a similar problem. Conquered two alien worlds, one with 9 million population and one with 0.05 million. Wanted to scoop up the 50,000 colonists and transport them to "resettlement camps" on the other world, but I'm getting the same error about not being able to complete orders. I guess I could always SM the population transfer and then zero out the population on the squatter colony.
It won't let you load -more- than the available amount of colonists. however, there is a way to do it. Pain in the ass, but still...
Basically, the number it shows you is rounded. So, tell it to load 45,000 colonists. Then, tell it to load 1,000 colonists, and repeat until it gives you the error. Then tell it to load 100, and repeat until it gives you the error. The colony should then have 0 population and be listed under "other colonies" (IE. uninhabited). I don't think Aurora tracks the population into the 10's, but it might be worth telling it to load 10 just in case.