Firstly, please ensure that the saddle height on your bike is set correctly. Assuming the position on the bike is optimal, knee pain during cycling is often caused by iliotibial band syndrome. Whilst riding the quadriceps in the leg do significantly more work than the hamstrings. This caused the quadriceps muscle to strengthen and tighten. As a result of this tightening the illiotibial band can rub over the top of the knee causing inflammation and knee pain.
The solution to this issue is regular stretching of the legs after riding and using a foam roller to help lengthen and relax the quadriceps and the illiotibial band