I don't know all the facts, but air pressure can change a lot with temperature and not all gauges read the same. I can put air in my truck tires in the am and go check them later without even driving and the pressure will be different up or down and also different between several gauges. If it was such a big deal you would think the ref would have said something or at least checked the pressure.
The ref does check the air pressure - they get the balls from each team about 2 hours before game time and inspect them for pressure and any other issues (scuffing, etc.). The teams can have used them previously but they have to be in "new condition". They apparently checked them again at half time after the colts complained about it and that's when it was found and corrected.
