Yup- check your form- are your knees going past your toes when you at the lowest position? If so- you're putting too much pressure on your knees. Make sure you are going back far enough with your hips so your knees aren't too far out in front(they should stay behind your toes when you squat down) and the pressure shouldn't be as bad on the knees. If you are dropping too low- beyond a 90 degree angle it will also put more pressure on your knees.
Make sure you aren't lifting your heels off the ground either when dropping down.