I just did... nada...
there's only one Aft Phaser 2.
as I'm sure there's only one Sensor Array in the Excelsior (which has the same problem), yet it appears offset too.
one thing that I might find common amongst them, is that I used the pick location tool to position them.
but still, I used that tool to position most of the systems, save a few major systems such as shields and warp cores,... and some do get offset, and some don't.
the impulse engine of the Galaxy is not even in a different mesh, so it can't be a problem with the structure...
and it doesn't seem to be a scripting problem because it still appears in stock QB
man... I hate when things just break for no reason
(EDIT: I just fixed the impulse engine of the Galaxy, by using the locate tool and manually shifting the engines to round number positions... but the same thing didn't work for the connie's phaser)
(EDIT2: the phaser is where it's supposed to be... .GetPosition() returns the right XYZ, as it's written on the hardpoint.. it's just being shown offset by the targetting reticle, and it's also being detected out of place by the damage system.... which is going to mess with the bit of armour tech I was going to adapt from FTech
)