It's this: the Correction Nine weapons were not actually designed by humans.
Why do I say this? Well, for starters, back in FTTP, we see the Falkoks with the (upgraded) C01r and the Ray Gun.
But also, the weapons just feel very... alienish. Take the C01r and compare it with other human manufactured slot 2 weapons. Where other slot 2 weapons sound tough and feel very brutish, the C01r sounds soft by comparison with a rather unique firing sound. It just feels different. I would say it is more similar to weapons like the alien rifle than other human weapons.
How do the humans have them? The humans basically copied and/or stole a bunch of these weapons from other factions that use them, like the Falkoks. This is not the first time this occurs in the series. The Usurpations are infamous for stealing Civil Security's weapons and equipment. It's not unlikely that humans will do the same.
If you want some more convincing, then take for example the real life Type 56 assault rifle, which is basically a Chinese AK-47, or the J-20, a rip-off of the F-35 (pretty sure it was built from stolen F-35 plans as well).
This may also be an explanation for why CO9 weapons are so rare. It's harder to build up a large supply of stolen weapons than it is to manufacture them yourself. Additionally, the extraterrestrial nature of the CO9 weapons can make them difficult for humans to mass produce.
Anyways, that's just a theory of mine, and it may or may not be true.