Other mistake: Before the Madame Amberly boss fight, Cortex shouts at Amberly, "I'm an evil scientist!" just before Amberly is about to say, "A scientist are ye? To me you'll always be a little bug!" For some reason you can see a quick flash of her in a "T" pose.
Other mistake: Partway through the game, the player reaches N. Gin's battleship. N. Tropy says "tell us where the treasure is and we'll let you go", which doesn't make sense as the treasure he is referring to is the Evil Twins' treasure; he has never met the Evil Twins and has no way of knowing about the treasure.