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)
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 Sacred Beasts - S3-E22
Plot hole: When Marcel is running through the underground chasm, Chazz emerges from a small passageway that Marcel passes. The last time Chazz was seen, he was one of the Duel Ghouls approaching Jaden at the end of the previous episode. Marcel only got to where he was so quickly because jumped and ran through a chasm he opened, so there's no way Chazz could have gotten down there through a hidden passageway before him. (00:03:35)
Plot hole: When Marcel is standing in an abandoned area, he hears Bonaparte shout his name. Adrian is then seen standing a short distance behind Marcel, and then hides once he sees Bonaparte approaching. There's no way Bonaparte didn't see Adrian. Even if Adrian hid, Bonaparte was already close enough to see Marcel, so he should have seen Adrian as well, or at the very least, seen him on his way to find Marcel. (00:17:10)
Plot hole: When Blair walks into Chazz's dorm, Hassleberry says "It's Blair" as if he knows her. However, Hassleberry has never met Blair and shouldn't know who she is. (00:19:15)
Plot hole: Jaden activates Miracle Fusion, allowing him to fuse the Elemental Heroes Flame Wingman and Sparkman in his graveyard to summon Shining Flare Wingman. However, Flame Wingman was never sent to Jaden's graveyard. He activated De-Fusion (allowing him to summon Avian and Burstinatrix) when it was about to be destroyed, which meant Flame Wingman was sent back to his deck and not his graveyard. (00:17:13)
Graduation Match: Part 2 - S1-E52
Plot hole: When Zane has Cyber End Dragon attack Rampart Blaster, Jaden activates De-Fusion, allowing Rampart Blaster to be sent back to his deck (and allowing Burstinatrix and Clayman to come back to the field). Later, when Jaden summons Shining Flare Wingman, he states that it will gain 300 points for each Elemental Hero in his graveyard. We are then shown eight Elemental Heroes in his graveyard, including Rampart Blaster, but this card was never sent to the graveyard, it was sent back to his deck. (00:09:13 - 00:14:43)
Plot hole: Bastion uses the special ability of Hydrogeddon, where he is able to summon another Hydrogeddon from his deck. He summons this monster by drawing the first card from the top of his deck, but there would have been no way for him to know if the card on top of his deck was a Hydrogeddon card. (00:12:35)
Plot hole: When the collection of rare cards is shown inside Crowler's jacket, the Fusion monster Ojama King can be seen as one of the rare cards. However, Chazz doesn't acquire the Ojama cards until later in the season, and he is unaware of their existence until he gets them. Also, the Ojama cards are depicted as relatively useless, unless used in the right way, so it is extremely doubtful that an Ojama card would be seen in a collection of cards that are depicted as rare and valuable. (00:08:11)
Plot hole: To escape from the students chasing after him, Damon jumps from a high ledge in the Duel Academy building and lands in the forest. Then he swings across vines at great speed, but somehow, the students all end up ahead of him in the forest, even though they were walking on foot. (00:05:30)
Plot hole: After discovering the cards tossed into the ocean at the docks, Miss Dorothy goes to Jaden's dorm to alert him of this. There was no real reason for her to go to him, seeing as how she had no idea if this incident was tied to him specifically. (00:09:05)
