I have currently been able to work with an athlete who has suffered from a chain of injuries. As we have learned, these injuries can be traced back to one main issue, which was found when analyzing his stance. After bringing the athlete through the FMS and asking him to perform a few other lower body/core exercises we were given a better idea of what would and would not be acceptable in the summer program put together for him and his team. Any pain with movement automatically deletes that from the program and a new movement should be used instead.
While working with this athlete, testing and otherwise, I noticed how important it was to read body language and facial expressions. Many athletes will not let you know when they are in pain for fear of consequence. Watching their movements and the faces they make when in certain positions should be a clue when assessing. It is also important to ask the athlete directly if they are experiencing pain, they are more likely to say yes or give some sort of clue as to what is being felt throughout the movement. As an educated coach this should be interpreted accordingly.
Reprogramming for an athlete is a great way to exercise knowledge. The movements are to be broken down, looking at muscles being worked and joint motions; in order to assess what exercises should be performed. Knowledge of the angles being reach of each joint is also very important when reprogramming. Many athletes will begin to feel pain once the joint reaches a certain point. They will be able to perform this exercise but should stop right before pain begins as not to cause discomfort or more damage. If they are not going to reap the same benefits it may be best to change the movement or remove it completely.
Above all, it is most important to watch form. As with the athlete I have been working with, body positioning is most likely the root cause of pain and imbalances. Making sure he sets up correctly and follows through the movement with proper form will benefit him the most during recovery. Getting him to engage different muscles will help him in the long run to becoming a better athlete.