in each safehouse there is JTF officer (who gives/shows you secondary missions for the district safehouse is in) and also there is board that shows you encounter locations (those give supplies for the BOO wing upgrades) for the district ... so check the safehouses, you probably haven't activated the board in some of them. Story missions will give you large part of resources necessary for upgrades, the rest you have to 'grind' doing the encounters (and secondary missions give XP only I think). But if you activated the boards in all safehouses, even with all the BOO wings completely upgraded you still should have plenty of encounter locations left on the map.
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