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)
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)
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)
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
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)
Continuity mistake: When Crowler is making a list of all the students in the gym on a clipboard, his right hand is positioned to the right-hand side of the clipboard as he is writing names. In the next shot, his right hand is positioned near the top of the clipboard. (00:03:24)
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)
Judai Revived!? A Brand New Journey - S3-E52
Continuity mistake: When Shepherd and Crowler are looking over the files of the missing students, in a shot focusing on Crowler from the side, he is wiping tears from his eye with a tissue. When the shot cuts, his hand is lowered. (00:02:49)
The Ultimate Face-Off: Part 1 - S3-E45
Continuity mistake: When everyone is standing around Zane's duel disk at the start of the episode, there is a shot showing the duel disk on the ground, that pans upward toward Syrus. In this shot, Zane's deck cannot be seen in the duel disk. Later, after Bastion picks up Zane's duel disk, in a shot of him saying to Syrus "our friends are still out there", Bastion briefly lifts the duel disk into frame, and the deck can suddenly be seen inside it. (00:02:24 - 00:03:55)
Conquering the Past: Part 2 - S3-E43
Continuity mistake: At the start of the episode, in the shot where Jaden's life point count appears on screen, there are four cards in his hand. A couple seconds later, there are five cards in his hand. (00:02:17)
What Lies Beneath: Part 3 - S3-E39
Continuity mistake: When the henchman attacks Zane's Cyberdark Dragon with his Great Moth, Zane puts his right hand (which is sort of clenched into a fist), over the left side of his face. In the next shot, his right hand is over the right side of his face. (00:02:10)
A Sight Unseen: Part 2 - S3-E36
Continuity mistake: When Axel runs away from the Supreme King after Jim is sent to the stars, Jim's duel disk can still be seen on the bridge in the wide shot. The Supreme King and his goons go back inside the castle, but in the next wide shot, the duel disk has disappeared. (00:20:26)
A Sight Unseen: Part 2 - S3-E36
Continuity mistake: When the Supreme King summons Evil Hero Infernal Gainer, in the shot of him turning the card so that Jim can see it, his thumb is positioned toward the right-hand side of the card. In a close-up, his thumb is nearer to the middle. (00:07:28)
