Mark of the ninja perfect kill problem.

Are you just talking about silent kills? It shows you a direction to drag your mouse after you click them.

If
I remember well, press and hold left mouse button, then drag towards the direction it shows.

In order to get a stealth kill you have to get behind the enemy you wish to kill (or if you have unlocked other kills, in those positions) and when the red left click symbol appears, click and drag in the direction of the arrow that appears. Later on in the game you can unlock outfits that remove the need to swipe in the direction (Path of the Hunter if I'm not mistaken).

Thought you were some kind of muppet half-way through, but then I saw mouse. It's pretty clear what to do if you are using gamepad.