A lack of ankle mobility is often one of the contributing components to a less than optimal squat. As a general measuring stick, you want to be able to squat with your thighs parallel to the floor. 

Unfortunately, this is very difficult for some. If you were to examine lower body mechanics, the hips, knees and ankles should all move at the same time and and the right amount when performing a squatting motion. If one or more of these areas are dysfunctional, you may end up with the inability to do the motion in addition to pain if you do not take care of it.