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)
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)
Hiwada Town! Yadon's Well!! - S3-E26
Continuity mistake: When Misty says, "I bet it hasn't rained here in months," Brock is holding the map towards the bottom, but in the next shot, he holds it in the middle. (00:07:18)
Hinoarashi! Catch It!! - S3-E25
Continuity mistake: When Misty asks, "Ash?" the combination of the grass and dirt changes. (00:02:26)
Big Panic! Kimawari Contest!! - S3-E19
Continuity mistake: When Ash says, "Water!" the puddle near the one under the leaking pipeline is more to the left of it, but in the next shot, it is more to the right of it. (00:01:40)
Continuity mistake: When Ash says, "Misty'll take good care of your Marill, you'll see," Wilhomena is holding her parasol with on hand, but in the next shot, she is holding it with two. (00:09:16)
Suggested correction: I rewatched the shots, and Wilhomena is holding her parasol with both hands in both of them.
Kikyo Gym! Sky Battle!! - S3-E15
Continuity mistake: When Pikachu agrees after Ash says, "Someday, I'll go back and see my old friend," his mouth is open, but in the next shot, it is closed. Also, Brock is to the left of Ash, but in the next shot, he is not. (00:06:32)
Dai Pinch! Madatsubomi no tô - S3-E14
Continuity mistake: When Zacky is excited to meet Ash, Lizzie's mouth is open, but in the next shot, it is closed. (00:02:50)
Continuity mistake: When Arielle lands on the bridge, she is on two planks, but in the next shot, she is on one. (00:03:49)
Continuity mistake: When Ash, Misty, and Brock turn to Woodruff after he says for Ash to wait, Ash's right glove goes from covering his thumb to not covering it. (00:02:23)
Continuity mistake: When Officer Jenny is first describing the situation, her strap is not over her right shirt pocket, but in the next scene, it is. (00:05:52)
Continuity mistake: When a servant says, "All the usual places," the blue-haired servant has his mouth open, but in the next scene, it is closed. (00:01:46)
Continuity mistake: When a man says, "Hey, that looks like amberite," the case with amberite is open all of the way, but in the next shot, it is partially open. (00:07:38)
Continuity mistake: When Officer Jenny says, "This is the cutest one on the force," the strap of her bag is underneath and to the right side of her right shirt pocket, but in the next shot, it is over and to the center of it. (00:05:32)
Revealing mistake: After Ash says that it is his and his friends' duty to show that it is wrong to use Pokémon for wrongful deeds, part of Pikachu is missing. (00:07:34)
Don't Touch That 'dile - S3-E1
Continuity mistake: When Professor Elm says, "So I suppose you know Professor Samuel Oak,"Misty's and Brock's mouths are open, but in the next shot, they are closed. (00:09:43)
Don't Touch That 'dile - S3-E1
Revealing mistake: When Officer Jenny takes Totodile from Ash's hands, her right hand clips through it and Ash's left hand. (00:17:50)
Continuity mistake: At the beginning, the front of Ash's hat is red, but in the next shot, it is instantly white. (00:01:11)
Hanecco's Jealousy! Battle in Big Prairie!! - S3-E21
Continuity mistake: When Ash says, "There's a couple of Gloom over there!" Pikachu's mouth is open, but in the next shot, it is closed. Also, Misty is not smiling, but in the next shot, she is. (00:01:29)
Happinas's Happy Nurse! - S3-E13
Character mistake: When Jessie asks if she can go to Pokémon Nurse School to become a nurse, the flyer she holds misspells Pokémon Nurse School as "Pokemon Nurse School." (00:07:53)