The most likely explanation is that you have injured your shoulder and later your neck at some point. With MS, pain is either a result of spasticity/spasms or paresthesia (phantom pain.)
I remember that I had the worst neck pain about two weeks after I had a car wreck. I woke up one day and could not move my head because it hurt so badly. I think injuries like that take a while to show up, because the body hasn't quite caught up to it yet.
If the neck pain is interfering with your quality of life, I recommend seeing the doctor.
Not a lot to go on here. What bring on the pain? What does the pain feel like, sharp or dull? Does anything make it worse or better? How long does it last?