Adaptation Induced Plot Hole / Yu-Gi-Oh!

• The manga had quite a few examples in the anime, which mostly owes to the anime's Duelist Kingdom arc being something of a Broad Strokes adaptation, trying to carry in as many manga arcs as possible that were necessary to establish the characters without going into great detail.
• In the manga, Yugi's grandfather was subjected to a nightmarish simulation of monsters attacking him after his duel with Kaiba, something that put him under so much stress that it hospitalized him. As this was cut from the anime, it appeared that he somehow lost a card game so badly that he had a heart attack. This is given a Hand Wave as the holograms and the shock of the torn Blue-Eyes being too much for him, but we see him duel or watch duels quite a few times afterward with no problems. Though he probably got used to them eventually.
• The vast majority of plotholes in the anime's Duelist Kingdom arc resulted from the very different interpretation of the devices the players where using. In the manga, the machine used for most of the Duels was called a Battle Box, a machine that basically looked like a small room with glass walls and a table inside, with the walls serving to project the holograms. When the players played the game, they sat across from each other, and the holograms created by the boxes were generally small enough to fit on the table, with monsters often being about six inches tall. However, the anime, in the interests of making things more dramatic and impressive, decided to create large arenas meant for Dueling, with the players standing on opposite sides of a machine the size of a tennis court, on battle platforms a good distance off the ground, and massive projection devices creating holograms of large, lifelike monsters and effects. This, naturally, created problems, due to a number of plot points hinging on two players sitting close to each other and the technology being cumbersome and small-scale.
  • Jonouchi discovering Mai's perfume trick makes less sense in the anime. In the manga, they were sitting relatively close to each other in an enclosed space, so it would make sense for Jonouchi to pick up on the scents. In the anime, there's quite a distance between them, not to mention that they're outside, so it should be impossible for Jonouchi to smell the perfume. (Of course, the trick itself is pretty implausible either way, as the smells should be all mixed together coming from the same deck.)
  • Mokuba stealing Yugi's Star Chips before the latter realizes what's going on makes a lot more sense when they're sitting across the table and Mokuba doesn't have to conspicuously run all the way to the other end of a fair-sized arena.
  • Kaiba claims that one of the reasons he created the Duel Disk is because it requires the users to stand a good distance apart. He believed that Pegasus could predict someone's moves, but thought it was probably a case of Pegasus being really good at body-reading and tell-spotting. Therefore, he guessed that if he could put a good amount of distance between him and Pegasus, and stick some life-sized holograms of monsters and cards in the way, it would make his body language and facial expressions nigh-impossible to read. Again, this makes sense in the manga, with short distances and tiny monsters (and also makes the Duel Disk even more of a quantum leap over everything before it). But the arenas in the anime already have players standing a considerable distance apart and summoning giant-size monsters. If anything, Duel Disks actually tended to leave players standing closer to each other and make the holograms smaller.
  • In the manga, Kaiba's dueling rings were exclusive to himself and his company, and Pegasus was only able to produce the smaller Battle Boxes, creating a need for him to acquire Kaiba's technology to make a lifelike, real-size copy of his wife. In the anime, Pegasus's dueling rings were nearly identical to Kaiba's, making one wonder why he needed Kaiba's technology if he already had an equivalent. The dub fixes this by having him need both the technology and the Millennium Items to bring his wife back to life, which he could only get through beating Yugi and acquiring KaibaCorp. Of course, it's still unclear how hologram technology would help with literal resurrection.
  • Inverted with Jonouchi's duel against Bandit Keith. In both versions, Bandit Keith cheats by pulling 7 Completed cards from his wristband. In the manga, Jonochi should have been able to look over the holograms and see Keith was cheating. The anime's giant holograms makes it easier to pull this off.
• Some of the Millennium Items are given one-time-only powers that they never had in the manga, such as the Puzzle being used to swap the souls of Bakura's good and evil sides, though this is phased out post-Duelist Kingdom. That particular power sticks out, given that the resolution to Battle City also involves a villain separating his good side into a different body and holding them hostage, but for some reason Atem decides to do it the hard way this time.
• Many cards changed card effects between the manga and the real game, and their changes were carried over to the anime as best they could. This often created problems with the show's duel scripting.
  • Big Shield Gardna in the manga is a Normal Monster that incidentally has 2600 DEF, while the real game nerfed it to switch its position after being attacked (and it has 100 ATK, so good luck). The anime followed suit, but didn't rewrite the duels to compensate, meaning that you still have situations where opponents try to get around its massive DEF by attacking directly or overwhelming it with pure stats, but not through the obvious method of poking it once and then taking it out with something else (which is what Yugi does during the anime version of the Final Duel against Yami Yugi).
  • The duel against the two Mask Duelists involves Mask of the Accursed, a card that negates a Spell and then does burn damage to the opponent over time. In the manga, it did 300 damage; in the real game, it was buffed to do 500. In the manga, this left Yugi with 1100 LP at the start of Lumis/Mask of Light's final turn, which meant it would have taken a whole four turns to burn him out. In the anime, Yugi's down to 500, so simply ending his turn would have resulted in Yugi losing (which was the actual objective), making it rather inexplicable that he surrenders in the face of Obelisk. That said, the dub changing the drop to a drop into a "Shadow Realm Vortex" indicates in that version, Lumis surrenders because he doesn't want to become a soulless zombie (though it didn't remove the part where they have parachutes).
  • In the manga, Valkyrion the Magna Warrior was evidently a Fusion, with it and the Magnet Warriors being explicitly compared to the XYZ cards that Kaiba used (presumably making Valkyrion an early iteration of what would eventually be referred to as Contact Fusion). In the real game, this was changed to Valkyrion being a main-deck monster that is summoned by Tributing the Magnet Warriors. The anime followed suit, and regularly depicted Valkyrion as a main-deck monster—Yugi uses it as a cost for Ritual Summoning twice, for instance—but didn't remove the fact that De-Fusion works on it.
  • In the final duel between Yugi and Kaiba in Battle City, Yugi uses the effect of Kaiba's Flute of Summoning Dragon to summon Red-Eyes Black Dragon at the same time that Kaiba uses it to bring out two Blue-Eyes. In the manga, Flute of Summoning Dragon's effect is pretty loosely-written, translated as "all Dragon-Types in the hand can be placed onto the field." Note that it doesn't say "your hand", just "the hand", making the idea that it can summon any number of dragons from both players' hands a possible reading. However, the anime had consistently depicted the card as using its real-world effect and had Kaiba explain the effect as such, where it summons two Dragons from your hand (in fact, in the Japanese version, you can even read its effect for yourself). This causes the whole idea that Flute of Summoning Dragon can do this to come out of nowhere. This error even carried over into the Viz translation, which similarly rewrote the effect to be more like its real-world counterpart.
• In the manga, part of the Battle City ruleset was that most Special Summoned monsters could not attack on the turn they were summoned. This is why Egyptian God Cards are never summoned from the Graveyard for attacks, because since they can only be directly affected by spells and traps for one turn, they would essentially just sit around for said turn unable to do anything and then go back to the Graveyard. The Winged Dragon of Ra was the exception, possessing an Instant Attack ability that allowed it to attack on the turn it was Special Summoned, which is why it's the only monster where the "dump and revive" strategy was ever used. The anime changed this to only Fusion Summoned monsters having that limitation, which raised the question of why Ra was the only God used in that manner. Furthermore, to maintain its "Instant Attack" ability, they had Marik use Vengeful Bog Spirit in that Duel, which stops monsters from attacking on the turn they were Summoned, and showed Ra bypassing it - and in the process, raising the question of why Ra has an ability that seems to exist just to counter one card. However, the anime also buffed the "Instant Attack" ability by making Ra capable of attacking during the opponent's turn. Right before Yami Marik's duel with Yugi, Jonouchi says Yugi will have to summon six monsters to get his God cards, whereas Yami Marik can do it with only one card. It makes absolutely no sense he would say this, seeing as how Yugi has a Monster Reborn card too, and could do the same thing. (If anything, Marik has to work harder; Obelisk and Osiris/Slifer don't require any cost to have high stats, while a Special Summoned Ra requires massive LP payment to not have 0 ATK.)
• Another trait of the Battle City ruleset in the manga was that it did not allow players to control more than five cards at a time (regardless of type), as opposed to the standard game's ten. This causes one particular Duel—specifically, Marik's Duel with Yugi while using his Slime Deck—to not make a whole lot of sense. In both versions, he controls five cards (Revival Jam to absorb attacks, Jam Defender to turn Revival Jam into a shield, Card of Safe Return to let him draw every time Revival Jam comes back, Infinite Cards to remove the hand size limit, Osiris the Heaven Dragon to gain ATK for all the cards in his hand). In the manga, this means he can't play any other cards. In the anime, he can still play cards, which raises the question of why he isn't using his gargantuan hand size to summon another monster and kill Yugi... well, aside from sheer idiotic egotism, anyway.
• The prelude to the duel between Yugi and Pandora has been changed between the manga and the anime. In the manga, Yugi reflects on why the Rare Hunters went to steal Jonouchi's Red Eyes Black Dragon: after a while, he remembers that the computer in the store where they went to get the Duel Disks has a database listing every duelist participating in Battle City and their rarest card, so he arrives to the conclusion that the store is actually Marik's secret base and goes there. Once inside, he's greeted by the Dark Magician coming out from the computer to tell him that Pandora is his true master, and then Pandora arrives and the duel begins. The anime instead changes it to a random clown luring Yugi towards Pandora's circus tent base, but kept the computer scene without any explanation on why the Battle City database would be stored in a random computer in a random building.
• The anime's revelation of the Duel Monster Spirit World in a filler arc (the monsters exist in a parallel dimension that has separated from ours over ten thousand years ago after a war) proved decidedly off when the manga revealed its own origin (the monsters were created by Egyptian rituals involving the soul during the reign of Atem's father about three thousand years ago). One could say that the existence of the former doesn't necessarily contradict the latter... except for Dark Magician Girl, who was explicitly shown to be the former in one arc (a prominent leader among the Duel Spirits and implied to have been around during the war) and the latter in the other (the apprentice mage Mana's ka spirit and therefore just an extension of her personality and soul). Are they the same person? How did she become independent? Did Mana pull something similar to Mahad? Is Mana some kind of reincarnation? Why is Dark Magician Girl light-skinned even as a spirit when Mana's ka isn't? For the most part, the anime just quietly avoids bringing up the Spirit World during that arc and hopes you won't notice rather than furnishing an explanation for how this happened or how these two spiritual arrangements coexist. For even more strangeness, she popped up again for a guest appearance in GX, which featured a Spirit World prominently... only her personality is clearly based on Mana (fun-loving goofy apprentice with a smart side) rather than her character in the filler arc (ancient dignified leader). And she maintains the same voice actress as Mana throughout all of this...
• While the rules of Shadow Game aren't always consistent, it is established that inflicting a Penalty Game requires you to defeat someone in a game first, which is why villains have to challenge Yugi in order to win the Millennium Puzzle. This causes some problems in the anime-equivalent of the Monster World arc; Bakura is able to seal Yugi and his friends' souls into their favorite cards before the game has even begun, makes a grab for the puzzle and only has to play a game when Yami Yugi steps in. In Monster World, this happened during the game as part of the rules. A similar problem occurs during Duelist Kingdom when Pegasus seals Mokuba's soul inside a card in front of Kaiba without playing a game. Again, this wasn't a problem in the manga since the Penalty Game happened off-screen.
• It's stated during the anime-only filler arc, the KC Grand Prix, that "banned" cards cannot be played on KaibaCorp Duel Disks; however, there is no explanation as to why the Rare Hunter's Exodia cards and many of the cards Rishid/Odion and Marik gave Jonouichi/Joey activate like normal, when they were stated to be fake and banned, respectively. By a lucky coincidence, the English dub made the former into "marked" cards and removed all reference of the latter being banned, sidestepping the issue entirely.
• During the anime's version of the Ceremonial Duel, Atem is somehow able to conduct another Battle Phase after he used Monster Reborn to resurrect Slifer the Sky Dragon during the Main Phase 2 even though he has already attacked during the turn using his Dark Magicians. This is because in the manga's iteration of the duel, Atem activated the spell during Yugi's turn in response to Silent Magician's attempt at attacking him directly and due to how the manga rules work, would have led the monster to attack Slifer and win Atem the game but due to the anime changing the rule to Normal Spell cards so they can longer be activated during the opponent's turn like a trap card at that point, this would broke the previously established rule regarding how spell cards work (and not to mention that they can't change it to something like Call of the Haunted due to the spell's symbolic meaning), necessitating the card to act like a Quick-Play spell that can be activated during the Battle Phase just for the moment, otherwise Atem would have essentially resurrected Slifer for essentially no purpose at all.

---