I think I understood the issue. You cannot kill all enemies on the enemy territory if you dont have a mission on this territory. Enemies in this case do almost Immediate infinite respawn. For example there is a viviro factory on the very first island. You just cannot go to this area and clear it. You only can do it when you are on the mission to clean up this territory and during the mission you can normally clear this territory. It seems the World in not that open as you may expect. You tighten to follow the scenario. I think this is a main issue. You cannot do anything what you want in terms of enemy areas elimination. I took me 3 hours to undersood that. I tried to clean up the viviro factory zillion times and ofcause never won. I read comments and I think in many cases beginner players are trying to do the same.
Maybe there is another bug with quick respawn, but I only found this game behavior.

Hope that helps the clean up some issues with similar situations on the map.