Drink lots of water somtimes joint pain can result from low lubrication, and be easy on it. I would also pay special attention to it during your pre and/or post stretch :) hope this helps.
Another thing that might help is trying not to sit with your knees torqued. i get knee pain because of how i sit a lot of the time, with my legs curled up next to me on the left side of my body, kind of tucked under im sure you know what i mean. Other then that maybe try another program that is a low impact for a week or so to give your knee a break.
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