Understood. Thank you!The side quests won't appear at all if you take all of Che's sectors. Those side quests trigger off the story and the map. So when the story reaches the point where those would trigger, it checks to make sure you haven't taken all Che's provinces and if you have, you won't get them.
Bottom line, if you want MG teams, don't do anything with the PME map until you get the story caught up.