I often hear 'crunching' noises in my shoulders and knees with no pain. My DH (a physical therapist), says that there is probably nothing wrong and some sounds are quite normal. However, if you're having pain, I would modify the exercise or do something else. I know that if I sleep on one side too long, I also tend to get pain in my shoulders that dissipates with time. If the pain continues or gets worse, I would go and see someone about it though.
Carolyn