Did the Machines in the Matrix use human women to have baby humans, or did they have some type of mechanical womb? It's clear, from the variety of humans we see in the film, that they kept some kind of genetic diversity, but was that intentional? Did the Machines have any kind of genetic planning in place to create humans who, if they were detached from the Matrix, would be more docile, or did they use random selection?
Since the Machines were keeping humans alive, they had to have some method of breeding more, but they couldn't just take humans out of their chambers and let them mate, so how did they do it? And once you get to that question, it seems only logical for the Machines to use genetic selection to create humans that would best suit the Machines' purpose.