Are the gauss STOs turreted?
I believe the gauss cannon functionality is that each cannon shoots 5 shots per 5 second increment (not 3?). So you should have 5x20=100 shots per 5 second increment. If you had quad gauss turrets you would have 4x5x20=400 shots per 5 second increment.
That still doesn't account for 600 missiles though. Do you have any ships in orbit that might also be firing? Or some other STO ground formation hidden somewhere?
Another thought... If you have high enough gauss tech (level 8 I think) it's possible your gauss cannons will be able to fire twice at an incoming missile volley, so in that situation you could have up to 2x4x5x20=800 shots in I think still a single 5 second increment. That could account for your 600 destroyed missiles.
