Agent Smith: I'd like to share a revelation that I’ve had during my time here. It came to me when I tried to classify your species, and I realised that humans are not actually mammals. Every mammal on this planet instinctively develops a natural equilibrium with the surrounding environment; but you humans do not. Instead you multiply, and multiply, until every resource is consumed. The only way for you to survive is to spread to another area. There is another organism on this planet that follows the same pattern... A virus. Human beings are a disease, a cancer on this planet, you are a plague, and we... Are the cure.
When Agent Smith is interrogating Neo, after Smith has sealed Neo's mouth shut and he is backed into the corner, when the camera cuts back to Smith you can clearly see a reflection in his glasses of Neo still sitting down in the chair.
In the entire film, there are only two "homegrown", real humans - Tank and Dozer. They both have names of machines.