* The use of GrandTheftMe leads to some FridgeLogic about the choice of victim. The criteria that the vessel be a healthy non-Duelist whose possession would hurt Yugi applies to both Anzu and ''Honda.'' Sure, she's the LoveInterest, but wouldn't a boy be a more preferable vessel? [[WebVideo/YuGiOhTheAbridgedSeries The Abridged Series]] would have a field day with all of the implications...
*** [[spoiler: Though in volume four, when the RA project nears completion, it appears that Anzu's body is merely being used as fuel to recreate Pegasus's body with The Wicked Avatar. Not that it matters too much in the end...]]
* Speaking of Volume 4, something happened near the end of Kaiba's duel with Yako... [[spoiler:Or rather, '''didn't''' happen. Specifically, the scene is as follows; It's Kaiba's turn, Yako has no monsters, [[WhatCouldPossiblyGoWrong two facedowns]] and 1400 lifepoints. Kaiba, meanwhile, has 3 Blue Eyes waiting in the wings, even if only one can attack. [[BondVillainStupidity Rather than go for the kill,]] [[ThereIsNoKillLikeOverkill Kaiba draws Polymerization and proceeds to fuse the 3 Blue Eyes into their Ultimate form.]] [[AssPull Then Yako does his thing by summoning up the 3 Blue eyes Kaiba just fused, with one card.]] Okay, but Ultimate has 4500 ATK to the regular Dragon's 3000, the difference is large enough for Kaiba to strike any of them and win the du-... Wait, he '''ENDED HIS TURN?!?!''' [[WhatAnIdiot No, there wasn't a single effect in play that would keep Kaiba from attacking, even his own virus card which he specifically planned for! This does not make sense, Ito!]] Cue Yako pulling a CurbStompBattle, [[TooDumbToLive meaning Yako very nearly succeeded with all his plans because of Kaiba failing to beat him.]] Aaaaaaall of Volume 5 could have been averted if [[IdiotBall Kaiba had just finished him off already!]]]]
** There was originally a rule that fusion monsters couldn't attack on the turn they are summoned. Kaiba probably had to end his turn after fusion summoning Ultimate because of that, giving Yako another turn.
** Which begs the question... Why bother fusing them? Why not just take the one Blue-Eyes White Dragon that could attack at that point and end the game with it? Anything he risks with that, he still risks with the Ultimate.
** Also... While the fusion attack rule was present in the original series, the [[AllThereInTheManual Special Rules section]] in the same volume, by the [[WordOfGod writer, Akira Ito,]] presents no such rule. Which... Really just makes it all the more baffling.
** Well, Yugi also had to wait one turn before attacking with his fusion monster when he dueled Yako/[[spoiler:Gekkou]] in the second volume, so it looks like the rule was in effect. Also, I thought Kaiba summoned the Ultimate Dragon just to humiliate Yako, which isn't really unusual.
** To answer the main question, Kaiba had a Field Card [[http://yugioh.wikia.com/wiki/Alpha-Wave_Emission Alpha-Wave Emission]] which prevents all monsters face up from attacking unless they were equipped with [[http://yugioh.wikia.com/wiki/Vaccination Vaccination]] to negate that Field Effect. Only one Blue-Eyes White Dragon was equipped at the time with the Vaccination card, so the other two could not attack. You are correct in that nothing else was stopping Kaiba's Ultimate Dragon from winning him the game then, but that unfortunately must be chalked-up to PlotArmor for Yako.
** That and Seto isn't new to holding the IdiotBall. In the Duelist Kingdom saga he could have defeated Yami by using a [[http://yugioh.wikia.com/wiki/Negate_Attack Negate Attack]] to earn that one turn he needed to win (he had one in the field), but he opted for treathening to jump from the tower instead...
* In the climactic final duel between Yugi and Yako, Yako manages to summon the Wicked Avatar, which [[GameBreaker always has one more attack power]] than the other strongest monster on the field. Yugi works his way around this by summoning Obelisk the Tormentor and activating one of his special abilities - sacrificing two other monsters to make Obelisk's power infinite. Had the monsters drawn there, no headscratcher would exist, but Yako states that the Wicked Avatar is in a different league to Obelisk and will still win, until Yugi brings out a spell card which adds 1000 attack to Obelisk. So... they both have infinite power, but the Wicked Avatar's infinite power is greater than Obelisk's infinite power, so Yugi adds 1000 power to Obelisk's infinite power so that the infinities are now equal. [[FlatWhat What]]?
** It's related to some particular rules regarding the God Cards, that are explained more clearly in the manga- Ra is a more powerful god than Slifer/Osiris and Obelisk, so their effects don't normally work on Ra. The Wicked Avatar is sort of the evil counterpart to Ra, so it has a similarly higher status, which in this case results in it initially winning when their attack points are both infinity. Yugi's equip spell "promotes" Obelisk one step up the divine hierarchy, meaning it's now equal standing to the Avatar.