Happens to me as well... always where the bar sits for squats and good mornings. Literally right on the spot. Mine ain't so bad numerical-wise, just having a loaded bar sitting on it does hurt some. Similiar thing happened to be when I was running all bodyweight assistance work w/a weight vest. Shoulder broke out in the same areas the weight vest sat. I suppose it has something to do with the pressure against the skin, bacteria and what not.
Just clean well and if its the severity calls for it, some kind of cream/scrub like suggested by Fazc.