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I believe that here's your answer. A tick happened, and since the NPC was stunned during the tick, it considers it being out of combat now. Thus, he is able to counter your attack, since it's an attack that you started anew (considering he was out of combat).
Sure he's out of combat, he's stunned. But the question for me is how is it that the NPC initiated the comabt (PC seems to have made no active effort to type "kill NPC") and still got the counterstrike?
And it's probably because the NPC can technically initiate combat with 0% PE, but since he got no attacks, the counterstrike trigger remains set and fires when the PC swings back.
Alternatively, the PC was on mode kill here and still managed to stun the NPC before striking the killing blow. Then with the tick happenening between those two events, the pc's attempt to finish off the NPC would result in a counterstrike like Shadow said.