Agent Smith doesn't know jumping jack shit about either biology or zoology. The equilibrium of animals in nature is forced by lack of food supply and premature death. It's not like lions sit around in a meeting and say, "you know, if we have fewer cubs, the wildebeest population might stabilize a bit more."

Animals moving into other ecologies due to continental drift or other geological changes wiped out entire classes of animals as they moved in. Somehow, nature survived.

But then, a representative of a sentient computer that somehow believes that human bodies are net energy generators will probably make a lot of errors in the realm of biology. ;)

BTW, the estimated rates of species extinction currently thrown around are another bit of "Fun With Statistics," extrapolating from "area-species curves" and other things. Basically, wild-assed guesses. Actual extinctions are something else again.

While the environmentalist list of "threatened" species--the concept of "species" being somewhat flexible--is almost infinite, the IUCN "Red List" states that only about 800 species in total have been confirmed as actually becoming extinct in the last 500 years.