Maybe it is that when someone is dead and you activate your screen clearing level 3 before they respawn you will get less kills. So if all the other players die and Heihachi activates his level 3 when no one has respawned he gets no kills.
You're right. Activating a Level 3 Super before someone respawns after a kill doesn't grant you that kill. But my friend wasn't in the middle of respawning. I don't know. Haha.