I’ve noticed that if the Missile Defense System is used along a Federation frigate’s Armada Drones that the Armada Drones will no longer shoot down missiles, but the MDS will.
The MDS has a greater range then the drones and with its short cooldown you would pretty much need two missiles coming in for it to work.
My apologies. Just watched a recording closely and saw the faint red beam. Hard to tell it was firing without any visual cool down tracking.