Well, I think that's more a question of how individual judges handle their events.
I personally don't see much difference between John saying, "You did that wrong" and John going to get a judge, who didn't see it, and having the judge say, "John says you did that wrong."
Generally speaking, I don't think it is the responsibility of the judge to police any game during an event. As I said above, I think the best solution is always for the players in that game to come to an agreement about what to do when a mistake is discovered. The judge is there for when they can't come to an agreement on their own and call for a ruling. But if the players don't call for a ruling, I think the judge should be careful about volunteering one that wasn't asked for. And I don't think it is ever up to a spectator to call for ruling that the players didn't ask for.
That said, if one player is taking unfair advantage of the other in a game (usually because of relative experience of just being a jerk) and the judge observes it, I think he should step in under conduct and sportsmanship considerations. And I don't think it is amiss for a spectator to call a judge over quietly to observe a game that one player seems to be playing unfairly in. But this is a lot different from a situation where Player 1 sets 6 gold or two "Limited" cards during Setup and neither player realized it until one of them has Marshalled.
Other judges may see it differently, but that's my general take.