The dots are apart of the the normal debug process so don't worry. They'll go away once you turn debug back off in the modules again.

What you're seeing, I think, for example would be what would happen if you debugged the CQB module. For instance, let's say you set CQB to populate 10% of the time. You'll then see a lot of "regular" marks on the map and after a moment, some of them will turn a brighter green. In fact, 10% of them would if I understand things correctly. Those indicate the 10% of currently active CQB locations while the others are the remaining 90% (which at that moment wouldn't have any units there).

At least that's what I understand. I may be wrong on the particulars but that's how I think it works.