I've tested this in daytime, pitch-black nighttime, blue-nighttime, etc. and this always occurs. I'm assuming that the silent movements with a lowered pistol while crouching may not be in, but the AI seems to hear your movements anyway. So it's probably an audible issue for AI or they just detect people in really close ranges.
Wonder if fixing this would also help with them seeing you through walls at close ranges too. :P