Balls were measure pre game and halftime. Not sure if they are numbered, so not sure of you can compare each measurement and be sure you are talking about the same ball.
11 Patriot balls were examined at the half. I presume the 12th was the Colts intercepted ball and no one wanted to count that among the evidence, though that doesn't explain why it couldn't be re-inflated. 4 Colts footballs were examined at halftime.
Natural occurrence matters because there is no other evidence of tampering. The Patriot employee in the bathroom/closet (was this ever resolved?) could have done something, but its far from clear he did. He did violate the rules by which the balls are to be delivered to the field. And he was fired.