Here is the list of rejected roms:
Mario & Sonic at the Rio 2016 Olympic Games Update v16 (US) (Loadiine): While the loadline rom has 'media', 'content' and 'code' folders the only reason why it's rejected is because there's nothing in 'content' folder, meaning that if you update the game nothing will happen to the game.
Super Mario 64 (Prototype): It's fake.
Super Mario All-Stars (Final Prototype): When rebuilded, the rom is identical to the final US version.
Super Mario Kart (Final Prototype): When rebuilded, the rom is identical to the final US version.
Super Mario World 2 - Yoshi's Island (Final Prototype): When rebuilded, the rom is identical to the final US version.