3. "It's a white rock."
The truck in the S.S Anne's port in Pokemon Red, Blue, Yellow and the remakes is perhaps one the biggest Nintendo mysteries. However, because it's so well known, I've decided to omit it in favour of a slightly more obscure oddity in the Pokemon universe: the white rock of Mossdeep City in Pokémon Ruby, Sapphire and Emerald.
When you head towards the Space Centre on the island, you'll come across a woman standing next to a lone white rock. If you speak to her, she'll tell you that the rock was put there as a sort of good luck charm to make all the rockets launched from the Space Centre fly safely, and that she likes to use wish tags. That seems pretty straightforward doesn't it?
Many people were not convinced. Curiously, you can interact with the rock, but it just yields the message "It's a white rock". The fact that you could interact with this unique and random object caused a surge of rumours about a potential hidden purpose. A particularly absurd one claimed it would initiate an event that allowed you to board a rocket and fly into space to do battle with the legendary Deoxys. Of course, all the rumours are false and in reality the rock serves no purpose at all.
But did it originally? The comment the woman next to it makes about the wish tags is intriguing because, as you may know, the legendary Pokmon Jirachi is partly based on wish tags. Also, note that in the following years, Pokemon Diamond, Pearl and Platinum were released and featured an event for Shaymin involving a similar, albeit much larger, white rock. Coincidence? Although in reality the Mossdeep rock does nothing, the unanswered question is: was it originally intended to be much more?