According to Wikipedia, the Mark Twain Riverboat jumped its track a few days after Opening Day in 1955:
Disneyland's opening day brought further problems for Mark Twain. Actress Irene Dunne, star of the movie Showboat, had trouble breaking a bottle of water (from many major American rivers) across the vessel's bow for her christening on Dateline Disney. During the riverboat's first official voyage, when the crowd moved to one side of the boat to view a passing scene of an Indian encampment or other sight, the boat would list from the side and water poured over the deck, as no one had determined Mark Twain's maximum safe passenger capacity.
This oversight caused the Mark Twain to almost capsize on a voyage a few days later when ride operators continued to wave more than 500 guests on board until the deck neared the water line. As the ship traversed the sparsely vegetated river route, it came loose from its track and got stuck in the muddy banks. Immediately, the park established a maximum capacity of 300 passengers, which remains in effect today.
Which begs my question -- has the Mark Twain ever jumped its track since? How about the other riverboats at the other Disney parks?