Continuity mistake: When the Duel Ghouls break open the doors to the tennis court and Hassleberry and Axel walk back inside, in the crowd of Ghouls, the first row appears to be an Obelisk Blue student, a Ra Yellow student and a Slifer Red student. In the next shot, a Ra Yellow is now seen where the Obelisk student was standing and an Obelisk Blue student is where the Slifer Red student was standing. (00:17:02)
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)
Unleash the Dragon: Part 1 - S3-E25
Continuity mistake: When Jesse breaks open the capsule, he picks up the Rainbow Dragon card inside it. In the shot of the capsule being opened, the card is drawn way too small, compared to every other time cards are shown in the series. (00:12:55)
Continuity mistake: When Pegasus is being fitted with the cyber-design interface and virtual reality headset, there are two cables attached to the left-hand side of the headset that are not attached to the duel disk on his arm. A couple seconds later, the two cables on the left-hand side are suddenly attached to the duel disk. Two cables on the right-hand side of the headset attached to the glove on his right hand also appear from nowhere. (00:00:13)
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)
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 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
Plot hole: When the Harpy monster begins carrying Crowler and Bonaparte, Jesse has his Sapphire Pegasus attack it. Once it is attacked, the monster drops Crowler and Bonaparte, but the monster is never seen landing on the ground, or anywhere for the rest of the scene. (00:04:58)
Judai Revived!? A Brand New Journey - S3-E52
Audio problem: After Chancellor Shepherd says that the grander mystery surrounding Duel Monsters may be the cause of the incident, Crowler says "That is correct", but his mouth doesn't move at the start of the line. It's only partway through the line where his mouth starts moving. (00:02:49)
Return of the Supreme King: Part 3 - S3-E51
Revealing mistake: After Yubel's life points go down to 400, she tells Jaden should he win, they will protect him. The shot after Jaden says "Protect me?", it cuts back to Yubel saying she has always tried to shelter him from harm. In this shot, the purple mark on her face cannot be seen and it is then suddenly animated onto her face midway through the shot. (00:11:37)
The Forbidden Ritual: Part 2 - S3-E41
Continuity mistake: When Aster runs in front of the main characters to protect them from Exodia, Jaden asks what he is doing, to which Aster replies "Saving my friends." When he says this, Crowler has his hands over Jaden's shoulders. The group then runs away, but in the next shot of Jaden saying "Aster", Crowler's hands cannot be seen on Jaden's shoulders. (00:18:40)
The Forbidden Ritual: Part 1 - S3-E40
Other mistake: In the English dub, when Adrian first looks at the Exodia cards, they are shown to have the Japanese text and artwork that are used in the original Japanese dub. Cards in the English dub are displayed differently, with the image covering most of the card and the text not seen. (00:03:18)
All For One - S3-E27
Other mistake: In the shot of the main characters falling through the portal back into the other dimension, Hassleberry cannot be seen among the group as they fall. Granted, Zane and Aster and Crowler and Echo wouldn't have been present in the shot as they were separate from the main group, but Hassleberry was with them so he should have been seen. (00:19:55)
All For One - S3-E27
Continuity mistake: When Zane approaches Aster in front of the Slifer Red building, when he stops walking, he is standing right beside the edge of the wall next to him. In the next shot, he suddenly jumps forward a meter, and is past the edge of the wall. (00:11:30)
Unleash the Dragon: Part 2 - S3-E26
Other mistake: When Jesse activates the spell card Prism Wall, just as he explains that "So Yubel and I, we both take damage", Elemental Hero Bubbleman can be seen on his duel disk, even though Jesse does not have this card in his deck. (00:18:30)
Unleash the Dragon: Part 2 - S3-E26
Continuity mistake: When Marcel activates Immortal Class, his left arm is extended as the face-down card rises. In the next shot, his left arm is suddenly bent so that he can use the duel disk. (00:13:48)
Continuity mistake: When Crowler walks into the Chancellor's office to see Jaden there, in the first shot of him, his head is upright. When it cuts to a closer shot of him, his head is suddenly shifted to the left. (00:01:09)
Breaking of the Sacred Seal - S3-E23
Continuity mistake: After Adrian realises Marcel was holding four of the five Exodia cards in his hand, Adrian comments "If you had drawn one more card, you would have completed Exodia" while holding onto Marcel's arm. In this shot, there is a small gap in between his little finger and his right finger. When the shot cuts to Marcel, the gap in between his fingers is closed. (00:16:52)
Return of the Sacred Beasts - S3-E22
Continuity mistake: After Professor Eisenstein explains they need to go to the tennis court for the inter-dimensional duel to take place, it cuts to Bastion saying, "There's no time to waste, let's move." At this moment, Hassleberry is behind Bastion to his right. But in the next shot, Hassleberry is directly behind Bastion. (00:16:30)
