It was Faro fucking things up again. You learn the first thing he does when he realizes the robots are out of control is order his team to try to find a way to regain control so he doesn't have to tell anyone he fucked up, wasting time. When that doesn't work, he orders all his factories to retool into producing non-autonomous weapons. By this point in history, no one has conventional weapons anymore, the US is already heading this way by with drones. It's not even called the "Military" in Horizon: Zero Dawn. It's called US Robotics Command. Imagine in 50 years we come across an enemy we can't use drones on, and the swarms ability to hack any robotic weapon they use means the swarm had grown to the point where even nuking them repeatedly only slowed them down (which they did try, it's mentioned in datalogs). Everything was just too little too late.
If Faro hadn't hid things so long, like the fact things were out of control, that the Horus classes were sucking up biomass (like the time it was caught pureeing the dolphin pod), first trying to regain control, then bringing in Elisabet, every step trying to escape culpability, then humanity might have had a chance.
