Usually caused when you destroy the facility as long you still have one slot of covert operation empty (meaning 2 covert ops still runs out of usual 3 from the mod).

This will cause the upgrade for extra staff slot for additional convert ops ("Monkey_ResistanceRing_Level_1" and "Monkey_ResistanceRing_Level_2") already "greyed-out" while the slot still not available or disappeared from the upgrades list, depending on how much covert ops running at that time.

To fix, you can use this command in console:

Note this may caused you to have extra resistance card slots too. So kinda a cheat actually since now you can have all resistance cards activated.