One possible explanation is something called "impingement syndrome." The idea is that moving the elbows both above and behind the shoulders may cause them to become entrapped in the bony structures around the elbow. Also, starting to rotate the shoulders at the moment when the muscles are strteched so much may put added stress on them.
In terms of how to fix the problem, the simplest advice is to just not do it.
One thing to keep in mind that doing this may be secondary to an effort to always keep the fingers on top of the ball (which I think is bad advice for this and other reasons). I find that it is much harder to do this if you face your plam toward 3B soon after breaking your hands out of your glove.