In a comment on one of the game's Miiverse posts, the game's director, Koichi Hayashida, apologized for the inconvenience and thanked players for their time. "In the interest of being as fair as possible, we decided to terminate the event without recognizing the fastest time," Hayashida wrote. "We sincerely apologize for this matter, particularly because the vast majority of people played fairly."
The exploit seems to be related to repeatedly pausing the game, as there is a short delay between when gameplay resumes and the clock resumes. In other words: wibbly-wobbly, timey-wimey.