Maybe they called the wrong number? Someone else could've been guilty.
To play devils advocate, these "phantom" calls happen several times a game on both sides... just the timing of these calls sucked and they happened to score on one of them, after the flag was thrown. It happens... good teams overcome.
That said, loved the reaction from the players and coaches. They took it in stride and moved on, didn't let it affect their play and didn't act out towards the refs. That's a sign of a well coached team.