Thanks- those links would be interesting coming from someone with your knowledge in this area...
Rodgers' Clavicle
"Any severe force on the shoulder, such as falling directly onto the shoulder or falling on an outstretched arm, transfers force to the clavicle. As a result, the collarbone is one of the most commonly broken bones in the body." Johns Hopkins
http://www.hopkinsortho.org/claviclefx.html
"The clavicle is easily fractured because of its subcutaneous, relatively anterior location and frequent exposure to transmitted forces. The middle third, or midshaft, is the thinnest, least medullous area of the clavicle, and thus the most easily fractured;
the lack of muscular and ligamentous support makes it vulnerable to injury. The usual mechanism of a clavicle fracture is a fall directly on the shoulder with the arm at the side." American Family Physician Journal
http://www.aafp.org/journals/afp.html
Without much muscle and ligaments to protect the clavicle, not much Rodgers could have done to prevent it and he fell the exactly same way these describe as a common mechanism of injury (with huge guys landing on top of him too).
Hamstrings
Here's a few hamstring links if you'd like to look through them. In general, you'll find a large prevalence of injuries with many factors being suggested as the reason for the injury, and the injury risk for a reoccurring injury is much higher. There's also a lack on consensus on how to treat them. The best one I found as far as treatment is the top link, but it hasn't got support in the four years it's been out (according to one of my professors who is one of the authors). I think the main point from them is that there are many suggested causes and treatments, but nothing specifically has tons of evidence.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2867336/
http://www.ncbi.nlm.nih.gov/pubmed/22239734
http://www.ncbi.nlm.nih.gov/pubmed/22239734
With Cobb's break, I haven't searched for any articles, but it's safe to say a there's nothing that would have prevented Cobb's injury. He took a helmet straight to the bone. Any loading such as running, squats, jumping, etc. strengthens bones so we can assume Cobb's bones were fine as has had to do a lot of those to get this far. Same with Matthews. If you take a big enough load to the thumb, you're going to break it. Teams aren't going to spend time doing thumb exercises anyway if there are ways to prevent it. When he broke it the second time, there certainly could have been an error in allowing him to return too early though.
ACL
"Several prevention programs have been developed in an attempt to decrease the incidence of noncontact ACL injuries. The focus of current prevention programs is on proper nerve/musclecontrol of the knee. These programs focus on plyometrics, balance, and strengthening/stability exercises." American Orthopaedic Society for Sports Medicine
https://www.sportsmed.org/uploadedFiles/Content/Patient/Sports_Tips/ST ACL Injury 08.pdf
Plyometrics, balance, and strengthening/stability exercises are somethings that I would think are normal parts of NFL strength and conditioning programs. If they aren't a part of the Packers system, then there could be some fault for putting players at a higher ACL risk.
But looking at the very high prevalence of ACL injuries across the league, which has been increasing in recent years, there's certainly room for improvement on ACL prevention.
http://espn.go.com/blog/nflnation/post/_/id/95723/inside-slant-big-spike-in-acl-injuries_
Hope these help.