It could be a motor pattern thing, so try some foot work drills.
It could be your body working around a lack of range of motion (anywhere starting from the floor moving up into your upper body). A tight plantar surface can put your ankle in a bad position, putting the knee in a less than perfect position. Over time developing knee pain. The person then does drills to fix knee pain, but the root cause is the tight feet.
The problem can be upstream or downstream of where the pain is expressed.
It is probably a bit of both. So use all of Gregs awesome resources for training and use KStarrs Mobility WOD (free blog) to diagnose and fix your feet (and other body problems)
You can start here for feet: http://www.mobilitywod.com/?s=feet