Slightly under extending you legs is fine, over extending them causes all kinds of aches and pains. If your feet are pointing down as you stretch to reach the pedals and you are rocking on the saddle it is likely you are over extending. I Had my saddle too high by mistake and it caused hip and shoulder pain as I was too tense on the bike and over stretching, knee pain is not uncommon for the same reason. Once I dropped the saddle back to normal it quickly went away.