Odd. I'm glad H1 didn't have such markers though. There's a certain pleasure to going looking for stragglers. And markers somewhat break your immersion in the game world, because unlike tracker info, they're something external to your actual sources of detection. Plus it's too much like babying you, the way you're being handed enemies on a plate.

The way things were handled in H1, there comes a point where Cortana will say "We should make sure the area is clear of Covenant stragglers", but if you don't do it within 130 seconds (based on my testing with PAL Xbox), the game just considers the area dealt with.