Continuity mistake: In her initial appearance, May is a little taller than Ash. In subsequent episodes, May is slightly shorter than him.
Other mistake: During the Pokérap, when the Poliwrath name is said, the Pokémon shown is actually Poliwag. Also, when the Graveler name is said, the Pokémon shown is actually Geodude.
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).
Suggested correction: It's because these episodes were aired out of order.
Character mistake: Brock states that the Diglett are plowing the ground and the Dugtrio are planting the trees, but the opposite is true (The Dugtrio are plowing, and the Diglett are planting).
Other mistake: Larvitar's weight is 158.7lb, but Ash can carry it in his backpack without any problems.
The Ninja Poke-Showdown - S1-E32
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. [This is a result of mistranslation. In the original, Japanese version Ash orders Bulbasaur to "blow it away." He didn't say Whirlwind. Still a mistake in the English version.]
Pokemon, I Choose You! - S1-E1
Continuity mistake: When the capsule containing the three Poké Balls first opens up, you can see the names of the Pokémon etched into the balls (in Japanese), but when Ash picks them up, the names are gone.
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. (00:05:30)
Hiwada Gym! Forest Battlefield!! - S3-E28
Character mistake: Ash's Chikorita is knocked out by Bugsy's Metapod in the Gym battle against him. Brock mentions that Ash's remaining Pokémon are Cyndaquil and Pikachu, and Ash says, "I'll save Chikorita for later and use Pikachu now." However, Chikorita is the Pokémon that was just defeated, and Ash's remaining Pokémon is actually Cyndaquil, as mentioned by Brock. (00:11:20)
The March of the Exeggutor Squad - S1-E41
Other mistake: The Pokemon Exeggcute is shown evolving in to an Exeggutor naturally. But the Pokemon Exeggcute can only evolve into an Exeggutor with the use of a leaf stone. In the Japanese version, there is a mention that something in these woods causes Exeggcute to evolve without using the Leaf Stone (when Exeggcute evolves, James even mentions that there is no stone). However, as this was skipped in the English version, it creates a plot hole.
Character mistake: During the recap, the narrator says that Ninetales had defeated Squirtle by using Ember, but Blaine ordered it to use Fire Spin. [This error doesn't appear in the Japanese version.].
Other mistake: Assunta's Ivysaur attacks Sparky too early, before the battle even started, not to mention Assunta haven't given it any commands during the battle.
Plot hole: Pikachu repeatedly defeats Ground-type Pokémon with Electric-type attacks, despite the fact that Ground-type is supposedly immune to Electric-type moves.
Factual error: When we see that Dodrio's neck is tangled, the configuration doesn't make sense. It just looks like two bands of neck, but it doesn't reflect what it would actually look like if it was really tangled.
Character mistake: When Mandi brings out Golbat, Brock says, "Kingler is really weak to air attacks." But Kingler's a Water type, which has no weakness to Flying-type attacks.
Suggested correction: Brock is saying that Kingler is vulnerable to attacks from the air, not that it is weak to Flying-type moves.
Flower Power - S3-E6
Continuity mistake: When the person giving flyers says, "It's a giant outdoor Pokémon entertainment festival!" there is a man in the background with a blue shirt, but in the next shot, he has a yellow one. (00:01:58)
Mystery at the Lighthouse - S1-E13
Other mistake: When Professor Oak goes to rotate his monitor, his right index finger is intermittently not coloured in. (00:09:15)
The Battling Eevee Brothers - S1-E38
Continuity mistake: When Pikachu and Eevee are first talking, the beam closest to the screen is smaller than the others, but in the next shot, it is larger. Also, there is a tree to the left of Pikachu, but in the next shot, there is not. Additionally, Pikachu is next to the plate of food while Eevee is one centimetre away from it, but in the next shot, he is two centimetres away from it while Eevee is three centimetres away. (00:09:48)
The School of Hard Knocks - S1-E9
Revealing mistake: In the English dub, when showing the front of the flyer, it has filler text that is not related to what it is about. Also, its Poké Balls are slightly transparent and its picture can be seen through it. (00:05:43)
Pokemon, I Choose You! - S1-E1
Other mistake: When Pidgey turns its head to see Ash with a Poké Ball, its head feathers beside its eyes are mistakenly coloured cream instead of brown. (00:11:36)