I don't see how over-tightening the barrel would cause the problem you mention, because the barrel has a pin or slot where it fits into the upper receiver, and the barrel nut tightens over the threaded portion of the upper receiver, so in theory the barrel shouldn't move to take the sights out of alignment.
I've built several upper receivers, and at first used a torque wrench, but it is hard to always get within the torque specs and align the barrel nut so the gas tube will fit properly through the nut and upper receiver. The problem is that you might be within the torque specs, but the gas tube won't line up, so you can either loosen the nut or tighten it up a little more to get the gas tube to go through. Most gunsmiths will admit they tighten it a little more rather than have a looser or less tight setup.
My guess without seeing the rifle is that the front sight housing may be off-center, or there may be problems with the rear sight.
As to future problems with overtightening the barrel, it could or might cause problems by overstressing the upper receiver. My concern would be that your shots would be off if the sights are off.
If it is still under warranty, by all means send it back to Bushmaster to diagnose and correct the problem.
