That would be very strange.
At each shot, the XP bar should flash and add one XP for the shot.
Furthermore, after the game, you should click your way out until you're back on the main window.
Do you see the pop-up window "Experience Points Earned" at the end? If so, compare your XPs before your last shot and after you're back on the main window. At that point, the "final" XPs are awarded - only 5 for a CTTH!