: Yeah, I'm not sure what it's counting.
Just checked. It's counting aliens. The level is designed to allow aliens to respawn. So you can clear out one area only to return and have another alien present.
In truth, you could have gone looking for those two to kill them only to find others appearing somewhere else in the time it took you to do this.
Anyways, the level is only set to Exploration so leaving them alive doesn't matter, as you both found out. Somebody (M1A1 guys) must have added an exit polygon in the area your were in. In the original game, the only exit polygon is in the large room with the view of the Marathon.
Cheers
Hamish