Full Blog: http://www.chirostrength.com/blog-1/squat-faults
Often times this side shifting seen in the bottom of the squat can be a product of favoring one side. This could be the result of compensating for past injuries, or being involved in a sport that is biasing one leg (think about kicking or rounding bases in baseball). To fix this, train each leg individually and create a symmetrical strength and feel before resuming your normal front or back squats.