Killing a soldier: nanomachine warning

Solution 1:

This happens (mostly) through the entire game. In some scenes, like the very begining of that chapter, if you sniper-kill the PMC to prevent them from killing the rebels, is very likely to trigger a caution stage, but they'll not be looking for Snake. I really can't explain it to myself, how do they know Snake killed the PMC and not the militia?, I don't know; even using a sniper might get you the attention of the PMC soldiers.

Snake's nanomachines are supposed to be a string apart from the one in the PMC soldiers (generations apart even), so they may have basic interaction but it's highly unlikely that they know Snake's actions through them. Furthermore, the militia know snake is helping them without them seeing him do so, and they don't have nanomachines, so that theory's out.

However caution mode will not get you an alert status (it'll get you closer to alert), but it will make it harder to stay in stealth, and if you're going for the higher ranks like Fox Hound or Big Boss, you shouldn't be killing anyone either.