According to some (un-named) coaches - this is fairly common practice throughout football, that's why the NFL allows "team balls".
It's one of those nod-n-wink rules, nobody ever bitches about it - until the Colts were down by 28 points, that is.
A bush-league gripe if there ever was one - like Billy Martin's pine-tar complaint - normally a non-starter, but some losers (like teams and theri fans not going to the Super Bowl) are gonna' find something to whine about..
All true but really the NFL should be the one supplying footballs and be in control of them throughout the game and this problem or any other irregularities regarding them would not happen. However it does provide fodder for talk for the runup to the SB.