Continuity mistake: At the end of the battle between Jaden Yuki and Gravekeeper's Chief, just as the explosion settles, in one shot you see the Gravekeeper's Spear card to the left of Gravekeeper's Chief on the duel disk. However in the next shot Gravekeeper's Spear is replaced with Magician of Black Chaos, which Chief neither has in his deck or ever played in the match. (00:13:35)
The Power Within: Part 1 - S3-E47
Continuity mistake: When Jaden has a vision of his duel monsters, in the group shot, Burstinatrix is a few meters ahead of Avian. But in the next shot, Burstinatrix and Avian are side-by-side. (00:04:19)
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)
Return of the Supreme King: Part 3 - S3-E51
Other mistake: When Jaden summons Elemental Hero Clayman in defence mode, the shot pulls out slightly and Jaden says "And now I activate Rainbow Neos' second ability." At this moment, Clayman can be seen on Jaden's duel disk, and the card is placed vertically on the disk, indicating that it is in attack mode. (00:06:55)
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)
The Ultimate Face-Off: Part 2 - S3-E46
Continuity mistake: When the purple bridge appears in front of the main characters, Ojama Yellow jumps on it. He is shown toward the middle of the bridge at first, but in the next shot, he is suddenly toward the edge of the bridge. (00:08:30)
The Power Within: Part 1 - S3-E47
Continuity mistake: At the start when the platform finishes rising, in the wide shot, Jaden is standing a short distance away from Syrus and Crowler. In the next shot, Jaden is suddenly closer to them. (00:00:02)
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)
Conquering the Past: Part 1 - S3-E42
Continuity mistake: When the main characters are walking through the wind in the opening scene, Crowler asks Jaden where they are going, to which Ojama Yellow replies to find Jesse. At this moment, Crowler has his right thumb pressed against his middle finger. But in a closer shot of Crowler, his thumb is pressed against his index finger. (00:00:12)
The Forbidden Ritual: Part 1 - S3-E40
Other mistake: When Aster summons Destiny Hero Dunker, in the shot of him showing the card to Adrian, its attack points are 1100, as shown on the card. The monster then appears on the field, and its attack points are 1200, as shown by the attack point display. (00:14:52)
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
Continuity mistake: When Zane and Aster see Crowler and Echo running away from the beasts, in the shot from behind the two, Aster is slightly behind Zane. When the shot cuts to an angle in front of them, Aster is slightly ahead of Zane. (00:05:04)
The Forbidden Ritual: Part 1 - S3-E40
Continuity mistake: When Zane is telling Aster about how he never got to duel the Supreme King, there is a shot focusing on Aster where he is facing Zane, then turns his body 90° to look at the others behind him. Then it cuts to a wider shot, where Aster is facing the others directly and isn't turned away from them. Then he's back to his original position in the next shot. The next shot, he and Zane are side-by-side, even though he was supposed to be facing him directly in the previous shot. (00:04:40)
The Forbidden Ritual: Part 1 - S3-E40
Continuity mistake: When Zane picks up Echo's necklace, in the shot of him picking up the necklace, his thumb is placed at the bottom of the pendant. But in the next shot, his thumb is over the top of the pendant. (00:06:32)
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)
A Sight Unseen: Part 2 - S3-E36
Continuity mistake: After the Supreme King has summoned Evil Hero Dark Gaia, just before its attack points increase to 4400, Dark Gaia levitates into the air a couple feet, with its left knee lifted upward. In the next shot, its knee is lowered. (00:18:33)
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)
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)
The Darkness Is Revealed - S3-E34
Continuity mistake: In the flashback of Jim as a young boy, he puts a stick in a mantrap, causing it to break. The distance between his hand and the top of the stick changes between shots. (00:04:55)
A Sight Unseen: Part 2 - S3-E36
Continuity mistake: After Syrus and Ojama Yellow keep walking toward the Supreme King's castle, the scene cuts back to Jim lying on the ground, while the King's goons laugh at him. Jim's left hand is next to his head in the first shot, but then it is further away when the shot cuts. (00:09:10)