Mislabelled shipments led to tariffs on uninhabited islands

I think they just looked at a list of ISO country codes. If you do that you'll find an enormous amount of your headspace is taken up by uninhabited and nearly uninhabited places.

That explains why they were listed separately, it doesn't explain how some ended up with higher-than-default tariffs. As the article points out, the other half of the puzzle is that sometimes people use the wrong ISO code (maybe a typo, maybe just guessing and getting it wrong). For places with little actual trade, such mistakes naturally make up the bulk of the trade volume recorded in official statistics.