Because when you go to take colonists from the planet, you need to know what race you are taking, and whether there is enough of that race to take, since the planet you're moving them to might not have the same CC for both races, and the alien colony likely doesn't have full political status. If you really want to merge the colonies, there is a SM button somewhere on the populations screen where you can edit what each colony has, just add the stuff in the alien colony to the human one and delete the alien one.