I've never tried to kick a FG, let alone under the pressure of a SB, so I'll let those who know more about that than I know criticize Gostkowski for the miss on the botched snap.
But, I think that ST in general didn't do their usual great job on KO's.
One of the real advantages that I always felt the Pats had in games this year...even if the Offense or Defense was a little off, was that their opponents often had to start deep in their own territory after a KO. The average Eagles starting position was outside the 25 yard line on Kickoffs.
The average opposition return of a NE KO this season was 18.9 yards.
The average return in the SB was 24.5 yards (not including a 10 yard penalty for an illegal block). That's 5.6 yards more (or 30%) per return in a game of inches.
The Pats never stuffed the Eagles inside the 20 on a kickoff, which they did often during the Regular Season and in other Playoff Games. Aside from the penalty play, the Pats only held the Eagles inside the 25 once (at the 23).
Little things add up to big things.