So I did some testing and figured out that the main issue that is causing it or atleast a solution is that AI are stuck in a prone animation when they wake up, normally shooting them or anything that causes an animation will cause them to fix themselves

There's a mod called https://steamhost.cn/steamcommunity_com/sharedfiles/filedetails/?id=1139830447 it's a surrender mod for AI (So if you see AI Get up and instantly surrender because they are greatly wounded or overun this is the cause) But it seems to help force AI into an animation when waking up because AI (And you the player unless you disable it in CBA) will now drop their weapons when knocked out and the AI pick them back up when waking up if it's not far away (Player still needs to grab it themselves)

The problem will still happen but it's much much more rare from my experience even when forcing it by constantly knocking an AI Out and waking them up