I agree. But side wall neck pocket being too small does not sound like a usage defect. I would still contact the Factory and have them explain what could have caused this to happenIt's not the nut. Music Man nuts are molded to shape and size and have a locating pin that sits in a matching hole in the slot for the nut in te neck that is cut by the same CNC machine that cuts the neck blank. That means that consistency of the string alignment at the nut is built in to the construction process with CNC accuracy. (If you ever need to remove a Music Man nut, don't try knock it out sideways but wriggle it upwards).
Even if it's out of warranty, it should not cost a lot for a good luthier/tech to gently enlarge the side walls of the neck pocket where required to make enough room for neck alignment. (Do NOT try to shave the neck narrower, it's a larger pocket that's needed).