GalCiv 3 Crusade and original base game:

It's possible to create free population when you have a shipyard within 6 tiles of populated planets and a ship with one or more colony (or transport) modules: when your colony ship leaves the shipyard, a fraction of the population drawn from each planet gets replaced. As a result, when you draw 3B pop from three planets with a total pop of 6B upon leaving the ship yard and return that pop to one of the planets, you may end up with a total of 6.5-7B pop.

The effect appears to be more pronounced when you have more planets in range of the ship yard, a higher total population, and a colony ship with higher pop cap. It doesn't work with only one planet, and I've occasionally seen cases with multiple planets where it didn't work, although I never found out what was different in these cases.

I've tested this with a custom race that is Synthetic and Prolific in the original base game as well as in Crusades. I tested it with the Terrans too, to make sure this is not race specific; but only in the original base game.

I'm not sure what determines the amount of free pop. But I doubt this is working as intended.