This is 3B umpire Charlie Reliford, who we believe is the crew chief, talking to a pool reporter. It pretty much jibes with what I posted here earlier,

“We had about six rules involved here. … As Felipe Lopez goes by second base, the home plate umpire (Larry Vanover) couldn’t tell if (Lopez) touches the bag or if the out is recorded when (Lopez) touches the runner. And that made a difference in whether or not the run counted. If (Lopez) had touched the bag — and we determined that that was an unmistakable act of an appeal — the run wouldn’t have counted. The extra time it took Lopez to tag the runner (Pierre) allowed the run to score.
“Joe (Torre) came out and said, `You know that run counts.’ But we couldn’t make that call until we knew exactly what we had at second base. They could have gotten teh fourth out with an appeal at third base (a player in possession of the ball touching the bag), but they didn’t do that before leaving the field.”