Head in the Clouds: Part 1 - S3-E7
Deliberate mistake: Chazz and Adrian take part in a duel where they stand on glass platforms that are suspended in the air, held by helicopters flying above them and are positioned at least a hundred meters apart. They appear to have no problem communicating back and forth, despite the large distance between the two and the helicopter rotors loudly spinning above them.
Head in the Clouds: Part 2 - S3-E8
Continuity mistake: At the end of the previous episode, the four cloud tokens that appear on Adrian's field are summoned in attack mode (as shown by the ATK on the point display). At the start of this episode, the cloud tokens are now in defence mode. (00:02:01)
Head in the Clouds: Part 2 - S3-E8
Continuity mistake: When Adrian uses Nimbusman to destroy VWXYZ-Dragon Catapult Cannon, Chazz puts his hand over his head when sparks begin emerging. When the shot cuts, his arm is lower down. (00:07:18)
Head in the Clouds: Part 2 - S3-E8
Other mistake: When Adrian passes out after the duel, it cuts to Jaden saying "Adrian" in concern. When he says this, he is looking directly forward, but Adrian is on a glass platform suspended in the air and Jaden is standing on the ground, so he couldn't have been facing him directly. (00:18:29)
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)
Trapper Keeper: Part 1 - S3-E11
Continuity mistake: After Hassleberry says "That could mean Jaden's in trouble", he lowers his hand away from his face. His hand is toward the top of his chest, but when the shot cuts, his hand is lower down. (00:00:41)
Trapper Keeper: Part 1 - S3-E11
Continuity mistake: When the students are queueing up outside the nurse's office, in the first shot of the hallway, a Ra Yellow student can be seen just outside the doorway, and behind him, an Obelisk Blue student can be seen. In the next shot, the Obelisk Blue student has been replaced with a Slifer Red student. (00:02:31)
Trapper Keeper: Part 1 - S3-E11
Character mistake: When Jesse is explaining Crystal Beast Amethyst Cat's ability to Trapper, he says "When I give up half my life points, you'll see what I mean." Amethyst Cat's ability allows it to attack an opponent directly by giving up half of its attack points, so Jesse was incorrect in saying he would be giving up half his life points. (00:10:30)
Trapper Keeper: Part 2 - S3-E12
Other mistake: When Jesse summons Crystal Beast Topaz Tiger back to the field after activating E Force, the Life Point count is displayed, instead of the attack point count that should have been shown. (00:04:30)
Trapper Keeper: Part 2 - S3-E12
Other mistake: After Jaden knocks the card out of Trapper's hand, an overview shot is shown where Jesse and Trapper's Life Point counts appear on screen. Trapper's life points are 4000, when they should be 1300 as he was attacked by Topaz Tiger earlier in the duel, and his life points went from 2900 to 1300. (00:15:50)
A Snake in the Grass: Part 1 - S3-E13
Continuity mistake: When the students realise that the doors are closing behind them, Jim, Hassleberry and Jesse's positions change when the shot cuts to a closer view of them. (00:07:33)
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)
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: When Jaden activates Fifth Hope, he removes five Elemental Hero monsters from his graveyard, shuffles them back into his deck and draws three cards. In the shot of the cards exiting his graveyard, Elemental Hero Sparkman is shaded orange. Since Sparkman is not an effect monster, it should be shaded yellow. (00:16:40)
Inter-Dimension Detention - S3-E16
Continuity mistake: When Syrus asks why there are three suns in the sky, Jaden is being carried by Hassleberry and Jesse. The next shot, Alexis approaches them saying "This is too weird" from behind, but when the shot cuts, she is walking behind, to the left of them. (00:02:45)
Inter-Dimension Detention - S3-E16
Continuity mistake: When Alexis is asking why Duel Academy became a sand box, she is standing in between Syrus and Jaden, being carried by Hassleberry and Jesse. A couple of shots later, when Jim is explaining how the land cuts off, the distance between her and the other characters is now much wider. (00:02:47)
Inter-Dimension Detention - S3-E16
Continuity mistake: When the tower begins to collapse, Syrus and Alexis are facing the tower directly, while Jim has his head turned to face the platform. Two shots after, when the shot cuts to focus on Syrus, Alexis and Jim, Jim is facing the tower directly, then is back to his original position when the shot cuts again. (00:03:11)
Inter-Dimension Detention - S3-E16
Continuity mistake: When the tower collapses, Alexis can be seen next to Syrus and ahead of Jaden, Hassleberry and Jesse. When they begin running away in the next shot, Alexis has disappeared. (00:03:17)
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)
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)