@Sheeps I originally noticed this problem while playing on my server and have been troubleshooting the cause ever since. I think the reason I didn't catch the problem earlier is because I'm estimating this to happen at about a 5% failure rate. If 60 units comprised of 4-10 OPFOR spawn, 1-2 groups may consist of vanilla fighters. You could technicaly play for hours and not notice the problem. Sometimes it's only a handful of soldiers on a map with well over a hundred or hundreds.
The easiest way I find to actually test this is to start the mission in the SP editor and then type player allowDamage false;
into the debug console and then click local exec. Then, through the commander tablet I enable teleporting and turn the debug on for the Virtual AI module. The map will then be filled with red enemy unit markers. When you teleport to these red markers and ALiVE virtualizes the soldiers, on the in-game map I hover my mouse over the soldiers and simply read what it says. This is much faster than physically trying to identifying them. If it says any word that begins with "Fighter" (example, Fighter AK47 or Fighter SVD), this is CAF Taliban. If the name says "Recon" or "Medic" or anything else, I know then it's a vanilla enemy.
Here's two missions. One is a super simple setup on Isola Di Capraia and the other, for anyone not inclined to download a map pack just to help me, is a slightly more complex mission on Takistan. The mod requirements are the same aside from the former needing the Isola Di Capraia map (I use AiA on that one and CUP on Takistan but CUP should work for both). The mods:
CBA
ALiVE
Spyder Addons
3CB Weapons
3CB Equipment
3CB Vehicles
3CB Units
CAF Aggressors
CAF Audio Patch
Burnes Foxhound (download link if needed: https://www.dropbox.com/sh/8kommnftolowc8f/AADMGYDJJ8Mtns3ZKbd8EbiCa?dl=0 )
CUP Terrains
Isola Di Capraia (for one of the missions)
https://www.dropbox.com/s/tmkh4h26cw9a2op/Operation_Hellhound.IsolaDiCapraia.pbo?dl=0
https://www.dropbox.com/s/3i9amoa8l1aq1s9/Parasol.Takistan.pbo?dl=0