As far as Murray, I would say that broken bones are a different category as I don't find as much fluctuation for that in player histories and I think anyone would have gotten injured on the tackle last year. The injury this year is likely a ligamentous injury of the foot so that is suspicious injury #1 to me. If he has another, I would not extend him.
As for Lee he had a muscle injury year 1, wrist ligament injury year 2 and now a toe ligament injury year 3. Add on 2 knee ligament injuries in college and I would suggest there is a clear history of tearing ligaments and his are probably not strong enough to have a long NFL career. I would do any extensions with him as heavily incentive based so as not to get caught with a ton of dead cap space should he need to be released due to recurrent injury.
As for Miles, I just believe it has to do with the way he is built with tight muscle fibers. I assume they have tried to strengthen his hamstrings and stretch them out as much as possible - if they haven't his trainers should be immediately fired. Now he seems to me to be lacking his burst this year and this accounts for people's perceptions that he just hasn't gone out and let it out when he has had the opportunity a couple of times and missed catches as a result. I believe that these instances are an indirect result of his old injuries and I think that he will never be that player again which means he is not worth his conract anymore.
As far as Miles $1.15M contract, I'm pretty sure this was a renegotiation where part of his salary was converted to bonus money and his salary number will be much higher next year. If it is just $1.15M again with no bonus money they you keep the guy and try to solve his injury problems with a new set of trainers. If he goes up to about $7-9M then I think his contract needs to be dramatically altered or he should be cut.