I dunno, for all of Chip Kelly's crazy ideas, his sport science stuff actually seems to work. The Eagles have been consistently one of the healthiest teams in the league for 4 years running now. And while you're right, stuff like bone breaks or random non-contact injuries are unavoidable to an extent, a good conditioning and medical staff can go a long way in preventing soft tissue injuries, which are what a lot of NFL injuries areHey I'm the one saying the Packers should hire Kaepernick!
Realistically, I think it's just the luck of the draw unless there's something truly systemic at fault that they're not doing for our players. Like I don't know how it could be a conditioning issue when somebody's collarbone snaps in half but another guy's doesn't. Same with concussions.
Muscle injuries might be a bit different if guys are getting hurt from overuse and lack adequate nutrition or rest.