The Adapted MACO rifle deals disruptor damage (and looks like a phaser) and the Adapted KHG rifle deals phaser damage (and looks like a disruptor)
As I also understand it, this is seen as a bug by the devs... and while I agree that the visuals should represent the correct damage, I dont think that the rifles should switch damage types.
I dont think that its too farfetched to believe that the Federation/Klingon's would want to adapt the other sides energy type in an attempt to see what makes it so good for them. They both do it for the Omega Adapted Technology set. They didnt change the type of torpedo to a Quantum/Photon or the cutting beam to a phaser/disruptor, so why do it with the ground weapons?
The Adapted MACO shotgun could be called a Phased-Disruptor Pulsewave Rifle (and have a green effect with an orange hue) and the KHG rifle could be called a Disrupted-Phaser Battle Rifle (and have an orange effect with a green hue). (Or whatever names you wanted to come up with)
Yea, maybe this is just me wanting to be able to use both the weapons and not gimp myself with having to remodulate more, but is it really that farfetched?