it's probably a problem with where you're holding it or your form, pretty common actually
I'd definitely look over the starting strength wiki (or videos), he goes over precise bar placement extensively:
http://startingstrength.wikia.com/wi...ifts#The_Squat
SquatRx is really helpful too:
http://www.youtube.com/view_play_lis...3D688F10C4DE1F
for me, I get shoulder pain unless I keep my back perfectly tight the whole time, with my shoulder blades back (sorta like you're doing a double bicep flex and showing off back muscles at the same). Like a lot of people I tend to slightly lose tightness in my upper back at the bottom of the squat, which can cause some pretty bad pinching on the way up. Watching the videos helped me a lot.