Keep an eye out for decoy soldiers
Enemy bases will often use decoys—blow-up dolls designed to look like soldiers—to screw with your head. You can recognize these by looking closely and seeing that they’re dolls, but also, if you’ve got the scanner upgrade for your binoculars, you’ll notice that they don’t actually have any skills. Because they are blow-up dolls.
Aim for headshots in Reflex mode.
Like Ground Zeroes before it, The Phantom Pain has an optional toggle called Reflex that will give you a few seconds of Matrix-style slow-mo reaction time once an enemy spots you. If you can take an enemy out during this Reflex period, they won’t alert the rest of the base. Do this by shooting them in the head. You can use a regular gun, a tranq gun, or anything else you’d like. If they’re wearing a helmet, aim for the chin and you should be able to get a headshot regardless.