After the game. If it was such an issue wouldn't it make more sense for Pagano to tell the officials to check the ball before each Patriot possession? This, to me, sounds like sour grapes from a sore loser.
They checked all the balls at halftime of the game, the 2nd half was played with properly inflated balls.
THere are mixed reports but ESPN says Pagano didn't complain during the game, there were several teams who had told the NFL what the Pats were doing, the Colts were presumed to be one of them tipped off by the Ravens. John Harbaugh denies tipping off the Colts, said he had no issue with the balls in their game against the pats.
the story has changed so many times I don't know but I had heard that Luck was tipped off by friends on the Ravens, and Luck told the refs early in the game and they have video of them throwing one of the Pats balls to an official to take and check for inflation. I've since read Luck was not involved at all so who knows.
But no they did not complain after the game, if they complained at all, it was before the game.
I really think people are missing the forest for the trees here, that one game is not the big complaint with "deflate gate" it's that there is now tons of data out there that suggests the Patriots lack of fumbles since the rule change allowing teams to bring their own footballs was enacted is WAY out there in terms of percentage of plays to fumbles. Nobody else is even close.
There are many possible reasons, the Pats are incredibly good at coaching players not to fumble, the Pats target players who don't fumble, they are just incredibly lucky since 2007, or they are deflating the footballs because it makes it easier for their players to hold the ball and not fumble.
I don't know how much detail they've gone into, Blount for example seems to have a similar fumble rate as a patriot and not a patriot, but he really hasn't had the ball that much.