Plot hole: Officer Jenny asks Ash what he knows about the "trio" when he tells her that the pirates are likely Team Rocket, but he hadn't said anything about there being three of them before that. And Jenny obviously didn't know anything about Team Rocket, either.
Factual error: When Venonat uses Stun Spore, Ash tells Bulbasaur to use Whirlwind. Bulbasaur just blows the powder away with his mouth, but he doesn't use the Whirlwind attack. He can't learn Whirlwind in any of the games, and what Whirlwind is supposed to do is to blow the opposing Pokemon away. Ash could have just as easily told Bulbasaur to blow it away, but he instead chose to tell him to use a move that he can't possibly learn. The only Pokemon that can learn Whirlwind are either Flying types or Bug types; i.e., Pokemon with wings (with the exception of Makuhita and Hariyama, which weren't introduced until generation III, and did not exist at the time this episode aired). In The School of Hard Knocks (Season 1, Episode 9), a character mentions information regarding a Pokemon's levels, attacks, and information which is taken straight out of the game, so it's very clear that Bulbasaur should not be able to use Whirlwind.
Continuity mistake: Ash suddenly has a Charmander, but his original Charmander evolved all the way to Charizard a long time ago, and we never see him get another Charmander. He couldn't have gotten another one, as we see each and every single pokemon that he catches within the show. Even in the Japanese-only episodes, he catches a bunch of Tauros, which Oak mentions when he returns to the lab.
Revealing mistake: When Team Rocket is running away with the trophy, James falls flat on the ground, and an indentation of his body as well as the trophy is made. The indentation shows a perfect match to the trophy, but James' arms were partially covering it, so there shouldn't be a perfect indent of the trophy in the ground.
Continuity mistake: Jessie seems completely surprised when she's told that Voltorb can explode, but in The Ninja-Pokemon Showdown (Season 1, Episode 32), not only did she and the others find out what Voltorb are, they were all affected by the explosions as well.
Character mistake: Misty is notoriously afraid of bugs. She makes this clear whenever bugs are around. She seems to be okay with Tracey's Venonat, but for some reason doesn't think it should be classified as a bug, when its type is Bug/Poison, and it's quite obvious that "Venonat" comes from "venom gnat, " a gnat being an insect. She even directly states that "At least they're [Venonat and Marill] not Bug types!"
Continuity mistake: When Meowth comments that Victreebel's Sleep Powder works well, James closes his eyes, tilts his head up, and says "Yes, we're a knockout combination." As he says this, his nose inexplicably grows to about ten times its normal length, but goes back to normal after he says the line.
Plot hole: When Team Rocket decides that they're going to capture Dragonite after it's been worn out, they appear in the blimp above the battlefield no less than ten seconds after they were shown in the stands. There is just way too little time for them to have possibly gotten up there that fast, even allowing cartoon physics.
Character mistake: When Team Rocket first sees Mandy doing his magic tricks, he produces a bunch of Pidgey. Meowth says "I like those Pidgeotto." He's dealt with Ash's Pidgeotto on numerous occasions, so there's no reason that he shouldn't be able to tell the difference.
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