Conquering the Past: Part 3 - S3-E44
Other mistake: By removing Cyber Valley and Cybernetic Hidden Technology from the game, Zane can draw two cards. The two cards are two individual Overload Fusion cards. He activates one Overload Fusion card, and at the end of his turn, he places the other card face-down. When Jesse attempts to attack, he reveals the face-down, which is revealed to be Dimension Explosion. (00:08:52 - 00:11:54)
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)
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)
The Power Within: Part 2 - S3-E48
Plot hole: Jaden activates Super Polymerization to fuse Elemental Hero Neos and Rainbow Dark Dragon to summon Rainbow Neos. Where exactly did Rainbow Neos come from? All the cards used in the Yu-Gi-Oh universe come from companies that developed them and the Rainbow Dragon card was only first made earlier in the season, so there's no way a monster that requires Rainbow Dragon as a Fusion material monster would exist. (00:17:43 - 00:18:43)
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)
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)
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)
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)