I've had this happen a few times, where enemies will spawn out of nowhere next to me. This was the Bunker level:
Ok. I wasn't sure how far the mod extends to changing things. Like I can throw the rock next to enemies and they cannot see me, however the moment I throw the rock (even before it hits anything) "THERE HE IS!" Makes the rock useless. I tested this in the Bunker level where you got the 4 Trijon in cages with like 5 enemies behind one way glass. The dude on the phone suggest opening the cages. Sounds fun right? Problem is it is literally impossible to reach that button without being spotted. I tried throwing a rock to distract them so I could sneak while they stared at the opposite wall, but they always instantly detected me when I did. Hilariously I can headshot a few of them through the glass and they remain clueless for a few seconds. All probably issues with vanilla, I just wanted to rant xD.