Clicking noises in your shoulder with or without pain can indicate an injury in your near future. Proper stretching and stabilization can prevent that impending injury, and get rid of the noises.
The body will speak to you if you care to listen, and if you’re hearing clicking noises in your shoulder it’s time to take action. Improve the alignment of the joint and all its moving parts with a well rounded stretching and strengthening program. 90% of the time I find that it is the chest muscles at the front of your shoulder that are the culprit for being too tight, and the rotator cuffs muscles for being too weak.