Fleet managers allow a planet to use fleets for defense, which is useful for defense. However, if you don't use a fleet manager on your planet and you have multiple ships in orbit, the offender must use a movement point to attack and destroy each ship. Whereas with a Fleet Manager, they only use one MP to attack. While a minor issue, this doesn't seem right. In some respects,it might be better to slow your enemy down with crap defenders while your main bases gear up.
The easiest solution would be to subtract a number of MP equal to the number of ships in orbit when a fleet attacks a planet with a fleet manager.