Many times issues in the knee actually originate elsewhere in the body.
To keep it simple, though, consider the fact that the knee operates between the ankle and the hip.
On the bicycle, one has considerable control over the ankle and the hip.
Try pedaling with the hip and buttock muscles instead of the thigh muscles (the thigh muscles transfer stress into the knee).
One can do this by imagining a strong rubber band between the heels of the two feet.
Focus on the left heel and buttock and push sideways with the whole leg as the foot descends in the forward portion of its circle.
If this has anything to do with your problem, it will disappear within a minute of mindful spinning and will return when you forget.