I think it is important to have an open line of communicate during sessions with your athletes and educate them. My athletes know that I would like them to tell me if any exercise causes them pain or discomfort. Instead of being scared and going through the motions on a particular exercise or causing themself discomfort and doing the exercise since I'm the boss and I perscribed it they know not every exercise is for everbody and there are many other options to accomplish the same thing.
With that being said I agree with what Eric Cressey has said in his Shoulder Saver Part 1 Article on t-nation. In summary he said…
Full Article https://www.t-nation.com/readTopic.do?id=1053531
Shoulder Saver #1: Avoid what hurts.
It seems logical, but we all know how tough it is to resist the exercises we've grown to love. Face the facts; you just might not be able to overhead press or bench with the straight bar.
Not all bodies are created equal in the first place; a good example would be the different types of acromions, a portion of the scapula. Those with type III acromions are more likely to suffer from subacromial impingement due to the shape of this end of the scapula:
These are the 3 types:
Type I Acromion: flat, minimal impingement risk, normal subacromial space
Type II Acromion: curved, higher rate of impingement, slight decrease in subacromial space
Type III Acromion: beaked, highest rate of impingement, marked decrease in subacromial space
Now, ask yourself this: when someone universally recommends overhead pressing, how often do you think they're consulting x-rays to determine if it might not be the best thing for you?
Moreover, not all bodies are equal down the road, either. If you're a type I or type II acromion process, you can "acquire" a type III morphology due to reactive changes. These changes may be related to a specific activity (e.g. weight-training) or just a case of chronically poor movement patterns (think of a hunchbacked desk jockey who's always reaching overhead).
There's almost always going to be something else you can do to achieve a comparable training effect without making things worse. So, the next time your shoulder starts to act up in the middle of a training session, put down the weights, take a deep breath, and walk over to the water fountain.
Use this stroll as an opportunity to recognize that something is out of whack and determine an appropriate course of action ??? including an alternative exercise. You might need to experiment a bit, but it'll come to you.