Various answers to my question about recovery time, "How much rest (tendon or ligament), for a novice? ", include information about the causes of knee pain, and how to prevent or avoid it.
I don't know whether to move that 'other' information into a separate question (perhaps CW). I'm not even sure if I want to; but if you want to (or if you want to edit the original question, or the question title, or the tags), please feel welcome to.
Perhaps there could be a new CW topic (e.g. "Several causes of knee pain") with many possible answers (too many days or too many hours per day; pre-existing condition; seat height; too cold; cleats in the wrong place; low RPM; ...?).