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)
Inter-Dimension Detention - S3-E16
Other mistake: When Chazz gets out of the hospital bed, he appears to be fully dressed, including wearing a jacket, trousers and shoes. There would be no reason for him to be dressed head to toe in that moment. Even if the nurse didn't remove any of his clothes, it would be unrealistic for him to be wearing his jacket, his belt or his shoes while resting in bed, and would've probably been removed when he was admitted. (00:06:10)
A Snake in the Grass: Part 3 - S3-E15
Other mistake: Jaden activates the spell card Fusion Recovery and brings back Polymerization and Elemental Hero Sparkman from his graveyard. When the cards are shown exiting his graveyard, Elemental Hero Avian is shown instead of Sparkman. (00:09:55)
A Snake in the Grass: Part 3 - S3-E15
Other mistake: Jaden activates the special ability of Card Trooper, sending three cards in his hand to the graveyard, so that Card Trooper gains 1500 attack points. The second card shown being sent to the graveyard is Ojama Yellow, but Jaden doesn't have this card in his deck. (00:02:40)
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)
Hanging with Axel: Part 2 - S3-E5
Other mistake: Jaden activates the spell card Contact Out to remove Elemental Hero Flare Neos from the field and summon Elemental Hero Neos and Neo-Spacian Flare Scarab from his deck. When he spreads out his cards to find the two monsters, a Fusion monster can be seen. However, Fusion monsters are never included in the main deck as they are only summoned when two monsters are fused together. (00:08:12)
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)
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)
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)
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
Character mistake: When Zane destroys one of Jaden's face-down cards, which is then revealed to be E - Emergency Call, he says "That was the trap, Emergency Call." However, E - Emergency Call is a spell card, not a trap card. (00:07:33)
Conquering the Past: Part 1 - S3-E42
Character mistake: When Zane destroys Jaden's Hero Barrier card with the effect of his Armoured Cybern, he says "Why wouldn't you play that spell?", but Hero Barrier is a trap card. (00:07:08)
Conquering the Past: Part 1 - S3-E42
Character mistake: Just after Zane destroys Jaden's Spark Blaster, he says "You were too afraid to fuse your Sparkman with your Spark Blaster last turn", however he used the wrong wording. "Fuse" means to combine two monster cards into one Fusion monster. He meant to say "equip" as equip spell cards like Spark Blaster are equipped to monster cards like Sparkman. (00:06:52)
The Forbidden Ritual: Part 1 - S3-E40
Character mistake: When Aster attempts to attack Adrian with his Destiny Hero Dread Master, Adrian activates a face-down card Dimensional Prison, to which Aster replies "Great, a Counter Trap", however, this card is actually a Normal Trap card. (00:17:05)
The Forbidden Ritual: Part 1 - S3-E40
Revealing mistake: Aster activates the ability of Destiny Hero Dunker, allowing him to send one Destiny Hero monster to his graveyard so that Adrian loses 500 life points. In the shot of the monster being placed into the slot where cards are sent to the graveyard, the bottom of the card is partially laid over the circular light on his duel disk beneath the slot. Despite this, the card remains completely straight and doesn't bend when placed over the light. (00:14:57)
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 1 - S3-E40
Character mistake: Aster uses his Diamond Dude's ability to activate Destiny Draw from his graveyard, allowing him draws two cards from his deck. After doing this he then refers to Destiny Hero Diamond Dude as Destiny Dude instead of Diamond Dude. (00:14:30)
The Forbidden Ritual: Part 1 - S3-E40
Other mistake: When Zane and Aster are looking through Jaden's deck, in the close-up of the cards, Super Polymerization can be seen. Aster then takes the card from the deck to look at it and rotates it 180°. However, the card was already right-side up when it was in the deck, so all Aster would've done is turn the card upside down. (00:04:18)