Continuity mistake: After Jaden and the gang leave Duel Academy, Marcel places a monster card on a duel disk. The monster card is in his right hand, but in the close-up of the card being placed on the duel disk, the card is in his left hand. (00:06:45)
Revealing mistake: Just after Crowler asks himself why all the important decisions fall on his shoulders, the shot cuts to Syrus, Alexis and Hassleberry. Hassleberry says "What'd you talk yourself into doing, Professor" and puts his hands on his hips. When he does so, his left hand passes through his trouser leg. (00:04:14)
Continuity mistake: When the students are all speaking with Crowler in the Chancellor's office, they are all shown facing the desk directly. They remain in the same position throughout the scene, but when Bonaparte runs into the room, they are suddenly facing away from the desk. (00:03:47 - 00:04:57)
Continuity mistake: When Jesse summons Crystal Beasts Amethyst Cat and Topaz Tiger, in the shot of them approaching the scorpions, they are standing right next to each other, at 45-degree rotated angles. In the next shot, they are no longer positioned at a 45-degree angle. (00:17:25)
Continuity mistake: When the scorpions begin entering the room, in the shot from behind Jaden and the gang, Jim is shown standing right beside Jaden. But in the next shot, Jim is behind Jaden. (00:16:55)
Other mistake: When Jesse summons Crystal Beast Cobalt Eagle, the Life Point count is displayed instead of the Attack Point count. (00:11:18)
Continuity mistake: When Adrian is tempted to let go of the rope, Jim puts his hands on the rope before Adrian can do so. In the shot of Jim putting his hands on the rope, he places his left hand over Adrian's left hand. When the shot cuts, Jim's left hand is on Adrian's wrist. (00:09:02)
Continuity mistake: After Jaden suggests they use their duel monsters to fly to the submarine, Jesse raises his right hand and tells him that the bio-bands are still draining their energy when they use monsters. When the shot cuts, his right hand is suddenly lowered. (00:07:00)
Continuity mistake: When walking to the submarine, Jaden stops walking and Jesse asks "What now?" At this moment, Jaden is standing with his body rotated 90° perpendicular to Jesse, but when the shot cuts to Jaden, he has suddenly rotated so that he is facing Jesse more directly. (00:06:50)
Continuity mistake: When Miss Fontaine hands Jaden the paper with the medicine list, she is holding it in her left hand at first. When the shot cuts, the paper is in her right hand. (00:03:23)
Continuity mistake: When discussing how to treat Blair, Bastion says "I'm sure a real hospital would be more than capable of helping her" and Jaden, who is sitting right next to him, turns his head to face Bastion. In the next shot, Jaden's body has rotated 90° and is facing Bastion directly. (00:03:00)
