This explains the totally janky behavior of the stun prod and baton in the 5 playthroughs of this game I've done over the past 25 years
If you first push yourself as close as you can get to the enemy model and attack the general area of their torso, it works every single time. But again, this is just me taking a guess as to what the problem you're referring to is!
It makes the difficulty curve super inverted
* Lockpicks: single inventory slot, stacking; plentiful; silent
* LAMs: single inventory slot, stacking; loud
* Dragon Tooth: infinite uses; can't break down every door; silent?
* Sniper rifle: optionally silent; semi-common ammo; can't break down every door
* GEP gun: loud; bulky; semi-common ammo
So torso hits from behind are the way to go.