The way the covert mission "Take Control" is worded "attacking one or more rebels factions", it suggest that you can use that benefit on more than one battle of the same turn before you have to return them to the supply.
Take Control of the Imperial Propaganda
+1 Military Science cube when attacking one or more rebel factions on your next turn (return it to the supply after any battles with other rebel factions next turn)
Sabotage Imperial Facility (x2)
Location: (2 unique cards) Trega, Mirzam
+2 Military Science cubes when attacking Sentinels on your next turn (return them to the supply after any battles with Sentinels next turn)