Over the years there has been huge controversy over the use of weighted baseballs and programs to increase velocity. Here is our analogy of what happens. After a period of time being on this program a player will see gained shoulder external rotation mobility and lost internal rotation strength. Weighted ball programs are effective at enhancing velocity not because of “arm” strength but because of hip/shoulder separation core strength increase from using the weight of the ball. When using a weighted ball to throw the front foot will plant and then a larger stress is placed on the core by delivering the weighted baseball. This is where players are seeing velocity increase come from the most. 
The problem with all of this is that this is not good on the pitchers arm because of these reasons: I believe this may be because it causes a quick and dramatic increase in external rotation, or layback.  Increasing this layback correlates to greater velocity.
This sudden gain in external rotation is not from a muscle stretching or the bone adapting. What is most likely happening is that the static stabilizers that are supposed to prevent excessive external rotation are being damaged.  This could be the capsule, labrum, or even rotator cuff.  These are not injuries that you want.  Plus, as layback increases, so does stress on the Tommy John ligament.
This is why many people do not get hurt during a weighted ball program, but end up getting hurt down the road.  They’ve pushed past their normal anatomy to increase pitching velocity.
So weighted ball programs have a few potential concerns: Overweight balls may be causing damage to the tissue of the shoulder to allow more layback. This gain in layback may also increase the strain on the Tommy John ligament and shoulder stabilizers such as labrum and rotator cuff.