Critical Research Failure: Despite his interest in playing the game and his knowledge about it, the author has made a number of research fails. These are just a few of them:
In the duel between Andy and Vladimir, Vladimir has Steelswarm Roach on the field. Vladimir says Roach can negate any of Andy's level 5 or higher special summons. However, Andy relies mostly on fusion summon, which almost always requires a card's activation that starts a chain to pull off. A card or effect cannot activate while another card or effect is resolving and summon negation must happen exactly when the summon happens. By the time Roach could activate its effect, the monster is already on the field and thus could not be negated.
The card "Queen's Machine" is used by Poison against Andy. One of its effects prevents Andy's machines from attacking his. In the story proper, Andy's monsters were able to attack Poison directly. Unless a card that prevents your monsters from specifically being attacked says otherwise or allows for direct attacks, in this situation Andy would be unable to attack period since Poison still has monsters on the field which his card dictates cannot be attacked by the opponent's monsters.
Harsher in Hindsight: Stan mentioned that turning against one's father is fairly common theme and that turning against the mother is practically unheard of, well...