back in the heyday of the Carnevil threads (a scant 1-2 months ago

), I had a similar issue ... like an idiot I went and started messing with the Screen and brightness/contrast adjustments and TOTALLY neglected the +5 voltage. it was way under 5.00, it was 4.87V. as soon as I up-ed the voltage it improved the accuracy of the guns SIGNIFICANTLY.
like the game behaved entirely different after correcting it.
I'd say a checklist of things to try though is first making sure your CRT glass and the overlay glass are both sparkling clean. check your gun optics too, and the little plastic eye piece, I had some Sega guns where the actual optic diode (whatever that part is) was bent out of place ever so slightly, and it totally wrecked the aim accuracy. as outlined above, make sure your +5 voltage is good too... the guns are dependent on this, and will be affected with not being able to register the outer areas of the screen well.
if that doesn't get it, remove the overlay glass, and step up the brightness/contrast higher than they were, and see if the condition improves any.
if it only affects 1 gun and not the other, try swapping the wiring harnesses (make player 1 -> player 2, etc.) and see if the problem moves.
if that doesn't get it.. well... tell us what kind of game you're dealing with. I can tell you Sega's guns are very finnicky.