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 Grinder Golem, or even 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.
An example from Yusei's second duel against Aki: Yusei has Stardust Dragon out and 2100 LP. Aki has her Black Rose Dragon, a Monster that can lower Stardust's ATK to 0, and an equip (Thorns of Hatred), that raises BRD's ATK to 3000, but it lowers other Monster's ATK rather than destroying them. You'd Expect: Aki to activate the Dragon's effect, lower Stardust to 0, and attack for game. Instead: Aki attacks with Black Rose Dragon, lowering Stardust's ATK and doing 500 damage, but not much else. Albeit, she was trying to cause as much pain as possible, but it doesn't really get much more painful than 3000 from Aki!
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.
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.