I think the NFL officials did figure it out before the game ended. Supposedly one of the game balls was taken out of circulation during the game by whatever the NFL calls the "ball boy" on the sideline and, from what I can tell, that's what is being investigated.
I can tell you from experience that a deflated football carries with it a major advantage, especially in inclement weather like the game last night was played in. As someone with fairly small hands, gripping a football can be very difficult. If I'm going to throw a football, I always have to deflate it a bit because otherwise I wouldn't be able to grip it. The NFL has strict standards as to how much the footballs have to be inflated to avoid giving either team any kind of a competitive advantage, and it would be a major infraction if the Patriots are found to have cheated yet again. I've even heard talk on ESPN that they could lose draft picks over this.
Now, that's not to say that this is why the Colts lost yesterday. It isn't. It lost because they are an inferior team. They play in a division that might be even worse than the AFC East, and they just happen to be the least bad team in that division. They lost because they have assembled no weapons around their mediocre QB and they just didn't seem to want it as much as the Patriots. Still, that's what makes the cheating by the Patriots even more disheartening. They don't need to do it, especially against a pathetic team like Indy, yet they do it anyway.