I'm guessing he's having you do this to lengthen your stroke and get you to keep from doing super short strokes that don't give you the full extension. I remember doing those years ago when I first started swimming again, but if it's hurting your shoulder I wouldn't do it. Just consciously think about not moving the other arm until the stroking arm gets to the top of the stroke (make it fluid, tho, the pausing would drive me batty).