Plot hole: After Ritchie tells Misty that he never talked to them through a phone, Misty could have put two and two together and realised that Ash was told to go somewhere by someone impersonating Ritchie and that he might be in serious danger. However, she does absolutely nothing to help Ash, she doesn't even inform Brock about it.
Bulbasaur and the Hidden Village - S1-E10
Other mistake: In the scene when Team Rocket tries to steal the Pokemon, Bulbasaur saves Oddish. Ash comes to help push Bulbasaur, and for a few frames you can see 2 sets of hand prints cut out where Ash's hands go.
The Mandarin Island Miss-match - S2-E18
Character mistake: Prima tells Jynx to use Ice Beam, but she very obviously uses Ice Punch. [This is actually a result of mistranslation. In the Japanese version she orders Jynx to use Ice Punch.]. (00:18:50)
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.
Haruka Travels Through Time!! - S9-E12
Revealing mistake: When Edna gets her parasol, it teleports to her. (00:05:34)
The Fourth Round Rumble - S1-E77
Character mistake: When Officer Jenny orders her Growlithe to attack Team Rocket's balloon, she refers to Growlithe as Arcanine. [This mistake happens only in the English version. In the Japanese version she refers to Growlithe correctly.]. (00:12:21)
Continuity mistake: In both "Attack of the Prehistoric Pokémon" and "Charizard Chills", Charizard carries Ash on his back without any trouble. However, later on in "Charizard's Burning Ambitions", Ash is suddenly too heavy for Charizard to carry.
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.
Character mistake: When Team Rocket first sees Mandi 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. [This mistake only appears in the English version. In the Japanese version Meowth doesn't even mention Pidgey nor Pidgeotto at all.] (00:04:49)
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 for anime physics. (00:14:30)
Continuity mistake: When Jessie says, "Guess we woke up this sleepy dump," she has lipstick on, but the next shot shows her immediately having no lipstick. (00:12:22)
Pokemon, I Choose You! - S1-E1
Audio problem: When Delia Ketchum says, "Oh, Ash, I'm so proud of you," the items that the Pallet Town townspeople are holding aren't being moved, however, the sound from banging of those items is heard. (00:07:35)
Character mistake: Misty is notoriously afraid of bugs. She makes this clear whenever bugs are around. She seems to be OK 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." [This error doesn't happen in the Japanese version.]. (00:03:19)
Other 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. (00:05:18)
What You Seed Is What You Get - S7-E1
Other mistake: When Poliwrath first appears in the Pokémon Trainer's Choice, its swirl mistakenly faces clockwise instead of counterclockwise. (00:12:13)
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)
Continuity mistake: When Ash is walking to the torchbearer, the people in the background change. (00:03:32)
Continuity mistake: When Ash first uses his Pokédex to learn facts on Snorlax, his right index finger is aligned with another one, but in the next shot, it is not. Also, his right ring finger is not aligned with another one, but in the next shot, it is. (00:07:40)
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)
Answer: Yes it ran away because Layla hurt its feelings.