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 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 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)
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 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)
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)
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)
Inter-Dimension Detention - S3-E16
Continuity mistake: When Jesse says to Jaden and Hassleberry that they should go inside, his body is facing toward Jaden, but when the shot cuts, his body is facing toward the academy. (00:05:38)
Inter-Dimension Detention - S3-E16
Continuity mistake: When Blair is explaining to Jaden that the creature scratched her with its hand, in the following shot where the scratch on her arm is shown, her legs are bare. Two shots later, she is suddenly wearing tights. (00:19:42)
Inter-Dimension Detention - S3-E16
Revealing mistake: When Chazz says Jaden can have his bed, a weird animation error occurs regarding the bed. There is a white bedsheet that covers the mattress, and a small shadow can be seen underneath the pillow and duvet. When he starts to get up, the bedsheet momentarily switches to the colour of the shadow midway through the shot. (00:06:10)
Inter-Dimension Detention - S3-E16
Continuity mistake: When the tower collapses, Alexis can be seen next to Syrus and ahead of Jaden, Hassleberry and Jesse. When they begin running away in the next shot, Alexis has disappeared. (00:03:17)
Inter-Dimension Detention - S3-E16
Continuity mistake: When Crystal Beast Sapphire Pegasus lands in front of Crowler and Bonaparte, there is a shot of the two of them screaming, where Crowler has his hand on Bonaparte's shoulder. In the next shot, his hand is suddenly extended. (00:05:02)
Inter-Dimension Detention - S3-E16
Continuity mistake: When Crowler and Bonaparte scream after seeing Sapphire Pegasus, they are shown facing the monster directly. There is quick cut to Sapphire Pegasus holding Winged Kuriboh in its mouth, but when the shot cuts after that, Crowler has rotated 90° and Bonaparte has turned around entirely to face the other characters. (00:05:04)
Inter-Dimension Detention - S3-E16
Continuity mistake: When Syrus asks why there are three suns in the sky, Jaden is being carried by Hassleberry and Jesse. The next shot, Alexis approaches them saying "This is too weird" from behind, but when the shot cuts, she is walking behind, to the left of them. (00:02:45)
Inter-Dimension Detention - S3-E16
Continuity mistake: When Alexis is asking why Duel Academy became a sand box, she is standing in between Syrus and Jaden, being carried by Hassleberry and Jesse. A couple of shots later, when Jim is explaining how the land cuts off, the distance between her and the other characters is now much wider. (00:02:47)
Inter-Dimension Detention - S3-E16
Continuity mistake: When the tower begins to collapse, Syrus and Alexis are facing the tower directly, while Jim has his head turned to face the platform. Two shots after, when the shot cuts to focus on Syrus, Alexis and Jim, Jim is facing the tower directly, then is back to his original position when the shot cuts again. (00:03:11)
A Snake in the Grass: Part 1 - S3-E13
Continuity mistake: When the students realise that the doors are closing behind them, Jim, Hassleberry and Jesse's positions change when the shot cuts to a closer view of them. (00:07:33)
Trapper Keeper: Part 2 - S3-E12
Other mistake: When Jesse summons Crystal Beast Topaz Tiger back to the field after activating E Force, the Life Point count is displayed, instead of the attack point count that should have been shown. (00:04:30)
Trapper Keeper: Part 2 - S3-E12
Other mistake: After Jaden knocks the card out of Trapper's hand, an overview shot is shown where Jesse and Trapper's Life Point counts appear on screen. Trapper's life points are 4000, when they should be 1300 as he was attacked by Topaz Tiger earlier in the duel, and his life points went from 2900 to 1300. (00:15:50)
Win Mr. Stein's Duel: Part 2 - S3-E10
Other mistake: When Elemental Hero Burstinatrix's attack points go from 1200 to 2000, the Life Point count is displayed, instead of the attack point count that is usually shown when monsters' points change. (00:11:49)