Sounds like a case of patellar tendonitis. When my adductors and VMO on the inside of the quad get tight it can cause pain on the inside of the knee and around the ACL which is something you should be careful with. Try rolling out your adductors and your entire quad as well as this video as you might be missing some extension of the knee joint. Your ankles could also be tight which is affecting how your knee tracks and further up the chain.

http://www.mobilitywod.com/2012/12/knee-pain-got-full-knee-powerrange-of-motionpotential-terminal-knee-extension-part-1/
http://www.mobilitywod.com/2012/12/knee-pain-got-full-knee-powerrange-of-motionpotential-terminal-knee-extension-part-2/