The simplest test in my opinion would be to raise your saddle a half inch at a time to see if that helps. I always know when I need to raise my saddle because when it's too low I get pain in the fronts of my kneecaps. Do try this before you experiment with more complex solutions. Using plain pedals is not going to 'cause' knee pain. Poor body position can certainly cause pain anywhere.
Am I assuming correctly that you have not been riding a long time? Many beginners have their saddles too low because they feel insecure when they can't put one foot on the ground while still sitting on their saddle. I don't know if this is true for you, since you are not giving too much information about your riding style.
Also, have you been straining your knees lately more than usual in other exercise? Slow and easy is good for avoiding joint stress.