controversial exercises

I've been working out with Fitness Blender for almost 2 years now and I love it, but I've recently heard some negative comments about a couple of the strength exercises and worry that I'm going to injure myself doing them. I know form is important but I've heard that back/chest flys are really actually bad for shoulders and can result in needing surgery in the future. I've recently looked up some alternatives and am trying to do those when the videos call for back/chest flys. I'm just wondering if anyone else in the FB universe has the same concerns or has any helpful ideas for modifications or alternatives.