Only when using that ammo. By chance, you have a magazine that holds 8. You load 8 in and fire that round in the completion of the stage, then the penalty is earned. In your original post, shooter did not “overload”. Absolutely nothing wrong with what they did to complete the stage, right up until they fired those two extra rounds. Had they stopped at the 14th round, dropped mag and cleared gun, there would not have been a penalty.
I hope that helps clear it up for you.