Where are you positioning the bar? High position (base of the neck) or lower position? (example of bar position: http://www.bodybuilding.com/fun/glen23.htm)

It could be a few things depending on where you position it, few ideas that come to my mind is leaning forward under the weight causing unnecessary strain on your neck as you try to correct your position. Also your grip might be too narrow so you don't have the best control of the weight causing the stress on your neck.

When it comes to squats I recommend not trying to fit into a recommended grip, simply position your hands in a way that you feel gives you the best control of the weight throughout the squat movement.