He had a mild stumble during the footwork and a referee might pause the program as it's considered a safety threat. I've seen it happen more in pairs (M/T at Skate Canada 2009). I don't think the ref would have stopped it (so close to the end), but he didn't want to take the risk.
Yeah, Joubert! Not his biggest fan, but it's great to see him go out there with his old confidence back and really sell the hell out of his program in front of the home crowd.