My left shoulder is messed up and will start hurting any time, for no reason, even when im just sitting there. Waking up is the most excruciating thing in the world; After a sleep is when the pain is worst. I didn't injure it exercising. It turns out the way the bone is formed is causing the pain. Going in for a second opinion in about 10 days. :\
In summary: You might see a doctor.