"Pops?" That sounds like bad news.
Here's what I looked up from NIAMS.gov
What Are the Signs of a Torn Rotator Cuff?
Typically, a person with a rotator cuff injury feels pain over the deltoid muscle at the top and outer side of the shoulder, especially when the arm is raised or extended out from the side of the body. Motions like those involved in getting dressed can be painful. The shoulder may feel weak, especially when trying to lift the arm into a horizontal position. A person may also feel or hear a click or pop when the shoulder is moved.
If he has a torn rotator cuff, I guarantee he will have complained of more than soreness, I doubt he could throw at all. I doubt he would be able to bear the pain of throwing from the outfield.
Pops in joints are usually a result of gases escaping the joint capsule, muscles or tendons moving, or rough surfaces. I think for now we can rule out the latter as it's not likely he has arthritis in his shoulder joint.
The 'pop' that people hear when they rupture their Cruciate Ligaments in their knee is a result of that ligament snapping. There aren't really any ligaments in the shoulder girdle that would rupture during throwing, and again, I doubt there would be multiple.
Sounds to me like he may have a little rotator cuff tendonitis, and as a result the muscular structure in his shoulder may be a little altered (some tighter than usual) or his throwing mechanics may have changed as a result.
Don't stress about this yet. I doubt VERY much we are talking a torn rotator.