You know, I remember having this problem a year or two ago, and I remember that I fixed it.
i may be being stupid here but is it not a hp problem ie the size of the phaser circle is too large
I'm almost certain it's something like this. Open the ship's HP (preferably in the MPE), open the properties for one of the phasers you notice has this problem and open the Subsystem Properties tab. There's a value for Radius. I'm like, 70-ish% sure that the radius of the phaser HP is too large. 0.25 is an example of what mine are set to, and I don't have this problem