That could be rotator cuff (the muscles in your shoulder) injury. The pain actually shows up down a few inches in the upper arm. There are exercises that can help strengthen the muscles and take care of the injury and pain. Just a thought....I screwed up both my shoulders during knee replacement rehab because I needed to use my arms to push up and get me standing after sitting. The exercises helped fix the situation.
P.S. sometimes it wouldn't bother me till I was going to bed at night.