Pokemon (1998)

So Near, Yet So Farfetch'd - S1-E47

Continuity mistake: When Team Rocket takes off in the boat, it sinks. Their pokeballs float away, and Jessie says "Arbok and Lickitung are floating away!" But she doesn't catch Lickitung until Princess versus Princess (Season 1, Episode 52).

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Pokemon, I Choose You! - S1-E1

Continuity mistake: When the capsule containing the three pokeballs first opens up, you can see the names of the Pokemon etched into the balls (in Japanese). But when Ash picks them up, the names are gone.

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Snow Way Out - S1-E64

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.

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A Chansey Operation - S1-E45

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.

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A Way Off Day Off - S2-E17

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.

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Show generally

Continuity mistake: In the early episodes of the Advanced Generation series, May is portrayed as being slightly taller than Ash. As the series moves on, May is consistently portrayed as being slightly shorter than him.

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