I've experienced that twice. The first time was about thirty years ago when I switched to fixed cleats. My feet rotate side to side a lot through my pedaling stroke, my left foot much more than my right. I developed pain in the back of both of my knees, the left so bad that I was eventually unable to ride. It took almost a year to recover from that once I figured out what the problem was.
Just this year I had some problems again in the back of my left knee and everything points to riding too far, too fast, and doing it too early in the year.
My first two rides were only around 25 miles each and I felt really strong. So, on my third ride of the year I decided to up the ante and rode 48 miles riding pretty hard through the first 40 miles at which time I started feeling a little pain behind my knees, and pain in front of my kness, muscle pain in my thighs....well, actually my hair was starting to hurt.
Most of that soreness went away within 2 to 3 days, however, the pain in the tendons behind my knees took about month to go away. I would think everything felt good, then I'd go for a ride and I'd start feeling some twinges if I rode too long or pushed too hard. I really had to take it easy for awhile.
At 14 weeks into the season for me I don't seem to be having anymore problems and I feel like I've dodged a bullet. My advice is not to let issues like that go on very long, or it could ruin your whole season..