Continuity mistake: When Bastion opens the door to his dorm room to let Jaden and Syrus in, the bag he is holding has a baseball bat sticking out of one side of the bag. A couple seconds later, after Jaden and Syrus have the formulas on the wall, in the shot where Bastion says "Most of these I've memorized", the baseball bat is now sticking out of both sides of the bag. (00:05:40)
Continuity mistake: When Jaden and Syrus are sitting at the Ra Yellow cafeteria with Bastion, in the shot where Jaden says "Well you deserve it", both he and Syrus have knives and forks in their hands. But in the next shot, the utensils in their hands have disappeared. (00:07:10)
Plot hole: After discovering the cards tossed into the ocean at the docks, Miss Dorothy goes to Jaden's dorm to alert him of this. There was no real reason for her to go to him, seeing as how she had no idea if this incident was tied to him specifically. (00:09:05)
Plot hole: Bastion uses the special ability of Hydrogeddon, where he is able to summon another Hydrogeddon from his deck. He summons this monster by drawing the first card from the top of his deck, but there would have been no way for him to know if the card on top of his deck was a Hydrogeddon card. (00:12:35)
