So I've spent a lot of time with this since last night and I think I've hit a brick wall. I even tried changing my faction to CUP Takistanis and I'm still having the issue with CSAT and IND Guerillas spawning (though note, I did not remove the CAF civilians).
So I did quite a few things, but the two most important.
1. I ran a test with CAF only on Stratis. No BLUFOR at all other than one player guy to teleport around with and interestingly enough I could not duplicate the issue. So obviously it's a mod conflict or bad script in my missions, right? Well...not exactly...
2. I jumped into AuTigerGrad's British Steel. The best part about that mission for this test is it uses identical mods to my missions. You can run his load order and launch my missions no problem. So surly I'd be able to duplicate this issue there. Except I can't. I cannot duplicate the error in his British Steel mission.
So I spent a good deal of time looking at the differences between his mission and my missions (I also removed all my mission files aside from mission.sqm to test). We definitely take similar approaches but still differences are there. For one, he's yet to have added the Intel on dead bodies. I removed it from mine and the issue still occurs.
He uses the 'only virtualize synced units option' and I use the other. I switched it and the error still occurs. He manually defines the units in the mil/civ modules whereas I rely on the preset platoon/company sizes. I switched it and the error still occurs. He has installations set for CAF to unused. I had it in medium and changing that did not help.
I've systematically gone through every difference between his mission and my missions and nothing I do makes this stop. If I consider maybe it's just a map issue (his mission is on Sangin) that's a fair, except this isn't just one map for me. This is on Takistan, Isola Di Capraia, N'Ziwasogo and Reshmaan Province.
The only thing left is maybe this is just a stupid mistake on my part and at this point I'd love if someone would take a look at my modules for me. If even switching factions isn't helping I'd have to assume maybe I made a mistake somewhere? The behavior is kind of interesting, when IND spawns I can see them briefly flash green on the map before they turn red and are then fully in the game world. For CSAT it's a bit different because they start red virtualized and spawn red too. Even when I let ALiVE virtualize them again, when I teleport back it's the same guys, sometimes even part of a CAF squad (so like 4 CSAT and 6 CAF in a 10 man squad).