Well, Mauer's leg muscle problems have never been figured out, as far as I know. That's a real mystery. Prior, unfortunately, had some bad luck with contact injuries that cascaded into connective tissue issues when he came back.
Speaking of great careers derailed by mysterious injuries, I always thought the world of Rocco Baldelli. Short of Hamilton on power, like most mortals, but just an awesome hitter with speed and D. Natural CF. Fatigue due to his cells being unable to pass waste out to the blood?