My head-canon is that one Christmas Eve in the 1940’s, a homeless war veteran was riding the rails and somehow found his way aboard the Polar Express. But his habit of roof riding proved to be his undoing when the train reached Flattop Tunnel before the hobo had a chance to bail out.
Later the same night, the Conductor, on his first Christmas Eve run, was on the roof checking up after a report that a man had been seen up there. Seeing no one, he turned to go back inside when he slipped on the icy metal roof. But he did not fall to his death.
The Conductor did not see the person who saved him, and when questioned, every member of the crew affirmed that it was not them. But ever since that night, no matter what perils encountered by those riding the train, no one has died aboard the Polar Express.