Anytime a bad guy(s) or security cornered a hero that has no way of defending themselves, the bad guy can take anything the hero has to offer. You'd Expect: For the bad guy to just kick the crap out of the hero without challenging them to a children's card game Instead: Yu-Gi-Oh Abridged sums up the entire idiocy:
Seeker: We are the elite group known as Rare Hunters. My name is Steve. And these are my associates. They are also called Steve. We're here to take your rarest card!
Joey: You mean you're gonna kick the crap out of me and steal it?
Seeker: No! First we're going to challenge you to a children's card game! Then we will kick the crap out of you and steal it!
Joey: Wouldn't it be much easier just to skip the first step?
A more direct plot element from the first series goes like this: in the middle of the ocean, the main characters' airship is attracted by a new villain totally out of the blue that demands that they defeat him in a virtual reality game thing (filler, anime-exclusive arc). They do it; but by doing it they left Evil Marik, the villain, unsupervised; and Odion/Rishid, the guy he's trying to kill, at his mercy. You'd Expect: For Marik to find Odion in the ship and kill him. And if Isis tried to protect him, kill her as well (seeing how she has no Millennium Item left to defend her at this point). Instead: He just sits and waits for God-knows-how-long, and near the end of the whole thing decides to leave the airship and destroy the arc villain's computers for the lulz. And go back on board.
The first ever duel between Joey and Kaiba takes place at Duelist Kingdom. It's the first ever duel using the newest technology created by Kaiba Corp. Kaiba summons a fusion monster with 2000 ATK, destroying Joey's monster, and is strong enough to do so to any of the monsters Joey had in his hand. You'd Expect: Joey would simply put monsters in defense mode. In case you didn't know, a monster in defense that's destroyed in battle deals no damage to the player's life points (with a handful of monsters having an aversion to this being their effect). It's been used before and after this duel. Instead:Joey keeps summoning them in attack mode. The monsters don't have HP like an RPG or anything, so being attacked by a weaker monster does nothing but cost yourself life points. Back when this duel took place, the rules were sort of different in a way that would have given Joey an advantage. There was no attacking directly, you could only attack as many times as there were monsters to hit. Joey could have simply put his cards on defense until he drew something strong enough to do something. Had Joey dueled correctly using the rules at the time, he likely would have only taken a total of 800 LP, out of a total (at the time) 2000. It would have kept going, but the idiot move was treated like Kaiba was genuinely skilled.
During the Battle City tournament, Kaiba has invented a new rule that disallows Fusion Monsters to attack during the turn it is summoned (Keep in mind that at this point, you can only fuse based on the monsters you control). You'd Expect: For the duelists to simply attack the player with all their remaining monsters before they fuse in the Main Phase 2. Instead: They fuse with the monsters first before they even attack and without even using Quick Attack. This results in most duelists throwing the game when they could have just attack first and fuse later.
Before the start of the series, Kaiba has been given a test by his evil stepfather, Gozaburo, into paying him back the $10,000,000 he lend him. At some point, he begins to leak out his plans to his stepfather about having to put him out of business so that he can take over KaibaCorp and makes him think Mokuba is the culprit of this. You'd Expect: That he would immediately tell his brother about this part of the plan. That way, Mokuba, while being accused of this act, won't have a reason to doubt him that he is a Manipulative Bastard. Instead: He brutalizes Mokuba without telling him about all this, accusing of selling him out, and sending him out of his room. He does all this in order for his stepfather to give him 2% of his share to be transferred to him when the time comes. Result: This scheme works a little too well, before it started to bite him in the ass. After having Mokuba captive and still believes in his brother despite this move, Noah, the filler arc villain, brings out a hologram of Kaiba where it rejects him. This breaks Mokuba enough for him to get brainwashed by him during the arc.
During Yugi's duel with Kaiba at Duelist Kingdom, Kaiba has played Saggi The Dark Clown A weak monster with only six hundred attack points and a face down card. Yugi Currently has Dark Magician on the field and drawing Gaia The Fierce Knight wonders why Kaiba played such a weak card. You'd Expect: For him to realize something is up and Kaiba's goading him into attacking with Saggi as Bait and not do anything. After all, Kaiba's a champion duelist, so he's likely got something planned Instead: He attacks and destroys Saggi with Gaia. Result: Kaiba reveals that Saggi had The Crush Card Virus put on him with the face down and activates it and monsters in Yugi's deck with an attack power over 1500 are forbidden from being played from now.
It's eventually made abundantly clear that the Big Bad of the third season is specifically targeting Judai's friends and loved ones in order to inflict maximum pain on him, and will continue to target them as long as they're made a target for him/her/it. You'd Expect: Judai's friends to agree to back off and not provide a target for the Big Bad, knowing Judai is The Ace and, with only himself going in to take care of the Big Bad, he has the best chance of doing so while cutting off the Bad's biggest advantage over him. Instead: They completely ignore Judai's pleas to this fact, dive in with him, and die off one by one as they become sitting ducks for the Big Bad.
Yet again when Judai is facing Yubel. Yubel has a card that allows her opponent to choose a card to put in her hand. Meanwhile Judai has finally found a way to defeat Yubel's nigh invincible monster with his overly powerful one. He equipped a magic card that allows him to bypass the ability that has caused him so much grief. So he then has to choose one of Yubel's cards to put in her hand. You'd Expect: Judai to pick Super Polymerization. Instead: He picks Mystical Space Typhoon. A card that destroys Magic cards. Such as the one that is stopping Judai from LOSING. Yubel does destroy it and Judai is in an even WORSE position.
Team 5Ds vs. Team Unicorn. Team Unicorn's starting duelist thrashes Jack and Aki, and does serious damage to Yusei before going down. Team Unicorn's second duelist runs a mill deck, reducing Yusei's deck to 4 cards before going down. Team Unicorn's last duelist finds himself in the position where ending his turn would have won him the duel, as Yusei has 0 cards left in his deck. You'd Expect: Him to actually, you know, do so. Instead: He decides he wants to win with honor or some tripe like that. So he attacks Yusei's monster, allowing Yusei to activate an effect that wins the duel for Team 5Ds.
It's not entirely his fault, though. Breo is the Second Wheeler for Team Unicorn. Both his teammates play very aggressive, offensively-minded strategies that deplete the opponent's LP quickly. You'd Expect: Breo to play an aggressive Deck as well, to finish off opponents weakened by Andore's raw damage. Instead: Breo plays a Mill Deck. Mill Decks are based around completely ignoring the opponent's LP. It's a good Mill Deck, but it also means that he'll effectively be fighting a fresh opponent, and that Jean's job isn't going to be made any easier. Result: Breo fails to deplete Yusei's remaining 2000 LP, inflicting minimal damage over the course of the Duel. As a result, Jean ends up fighting Yusei basically fresh.
Team 5Ds vs. Team Ragnarok. Harald is shown to have Interdimensional Matter Transporter in his hand, a card that removes from play one of his Monsters for a turn. He also has Birthright and Soul Resurrection in his hand (itself a What an Idiot, since both those cards are useless in his Deck). He needs to discard a card to activate the effect of Valkyrie of the Nordic Ascendant. You'd Expect: Harald to discard one of his junk cards and Set IMT as a precaution, since it has the potential to save one of his monsters from an effect that would destroy or weaken it. Instead: He discards IMT and leaves Birthright and Soul Resurrection to sit in his hand and do nothing. Result: On Harald's last turn, Yusei activates Zero Force before Gjallarhorn can trigger, reducing the ATK of all Harald's Gods to 0 and causing it to deal no damage. Had Harald activated IMT in response, he could have removed from play one of his Gods and Summoned it back during the End Phase with full ATK, winning the game.\\