I'm going to try my best to explain what may be the situation.
If it's not registering your hits half then it's kinda of hard to explain since I don't get this problem a lot. Usually this will happen if you take too much time and the enemy recovers and quickly moves out of the way, but this hardly ever happens. If you're too far back and the enemy is tumbling backwards then it may not register your hits sometimes. If you are 1, 1.5, or 2 feet from the enemy and the prompt comes up or if you wait 1 second before pressing the button then the game may not register the hit. The best way to fix this is to get up close and personal with the enemy and then press the button. You will have a better chance of hitting an enemy by doing this. I don't know if this is how it works as it dosen't happen to me very often.
NOTE: The following information is only for use on enemies when you shoot them in the head. This information is useless if you decide to perform a melee attack on an enemy who is shot in the arm or leg. If this infomation does not help, is lacking, or if you need more information, I'll post some more information on what may help you or you may need.