An incorrect body positioning on the bike can cause fatigue and pain in the neck and shoulders. For example, a bike positioning which is stretched out (reaching too far to the bars) will cause undue pressure on the upper body by shifting the weight forward. Make sure not only the bike is the right size for you, but take note of any pressure points and upper body pain when riding or during a fit session.
Ultimately, when a saddle is uncomfortable, one of the first things most people do is to just bring the nose of the seat down a degree or more to help relieve pressure from the sensitive soft tissue. When doing so, they ignore the potential extra pressure that is now being transferred to the upper body. Bike fitting is a delicate balance between pressure points and comfort. If your saddle is so uncomfortable that you have to tilt the nose down so much that you are feeling neck and shoulder pain from the increase in pressure in the upper body, it is time to rethink the saddle. Find a saddle with the correct shape and cutout for your style of riding. Having a saddle that supports your core and correct riding position is crucial to overall bike comfort. Be sure to find the correct saddle for your body; be sure it is comfortable in a position that balances pressure as opposed to a saddle that brings too much pressure either to the crotch or the neck and shoulders.