This seems like a good explanation from a scientific perspective: http://dailycaller.com/2015/01/23/physic...nce-video/
Based on what Brady has said in interviews (that he prefers the ball inflated to the NFL minimum) it's perfectly reasonable to expect the balls to become "deflated" due to the temperature outside changing the pressure in the balls. If the Colts had their balls inflated to the NFL max (or near to it) then their balls would also deflate, but not to below the NFL minimum.
Based on what Brady has said in interviews (that he prefers the ball inflated to the NFL minimum) it's perfectly reasonable to expect the balls to become "deflated" due to the temperature outside changing the pressure in the balls. If the Colts had their balls inflated to the NFL max (or near to it) then their balls would also deflate, but not to below the NFL minimum.