I agree with the ruling. Godzilla is supposed to give the ball back when you Save New York after the flippers go dead. The ball didn't return back and went straight to bonus count. Could this be a bug from a grace period shot while the 2nd ball is draining? In any case, the IFPA rules clearly state:
A major malfunction is a gameplay problem with a machine that results in the premature loss of ball in play in a fashion that is not a normal feature of the machine’s gameplay. These may be unusual one-time events, or they may indicate a recurring problem that will need to be addressed by technicians.
He should be getting a compensation ball because of this malfunction. I think the timing of this ruling was not ideal. I think it should have been ruled on when it happened and not after Jim blew up his next ball. But I don't think the IFPA has any wording in place that says that a ruling should take place immediately after the incident.