If you are experiencing any pain or discomfort then it would more likely be due to lateral movement of your knees. Your legs are designed to move forward and backward about the knee joint but not side to side. Even slight lateral movements can be enough to cause inflammation. More severe movements can cause ligament damage.
The tendancy during squats if for the knees to move either inwards or outwards during the upward portion of the movement. This is especially true when the squat is deep. Even more so when heavy weights are used.
Next time you do your squats, have a look at the position of your knees during the entire movement. If there is lateral movement, reduce the weight and/or don't go as low until you can correct your form.