Different leaderboards are managed by different moderators. I myself as a moderator require proof before I verify anything, and even then I watch the material thoroughly to make sure it's not TAS or anything, and that nothing against the rules was done. Some other moderators aren't quite this strict. With this issue, I'd recommend contacting the moderators of the leaderboard, specifically the mod who verified the run you're talking about.

To be honest the IL boards for Super Mario 64 DS are for show; they don't track who really has the world record since nearly all of those are probably in a full-game run anyway. The same goes with a lot of games with IL boards (except C&C and StarCraft 1 >:3).