One of the most blatant examples was in the first season episode "The Kangaskhan Kid", where in the Japanese version Tommy stares at Misty's breasts and asks if he can suck on them,note Keep in mind, she's ten. but in the English version the close-up on her chest is removed and he asks if they're people or Pokémon. He still gets slapped. Some fans, such as Suede, view this change as an improvement, since they didn't think the original joke made much sense to begin with.
On another note regarding Pokémon: The Series, the title is sometimes accused of being the product of bowdlerization due to the original Japanese title translating to Pocket Monsters. In reality, the localized title was a portmanteau to dodge legal issues with an existing toy line called Monster In My Pocket. The term "Pokémon" is used all the time in the Japanese originals, though; it wasn't invented by the translators. "Pocket Monsters" rarely ever appears other than in the titles of the anime series and some of the games. Pokémon Diamond and Pearl acknowledge that "Pokémon" is short for "Pocket Monster" in the English version. A minor NPC mentions that the "Pokétch" is short for "Pokémon Watch", which ultimately makes it short for "Pocket Monster Watch".
The US intro uses clips from the Japanese intro but changes the lyrics and context. When Pikachu runs between a girl's legs, the original lyrics are, "Even through fire, water, grass, forests, earth, clouds, that girl's skirt."
4Kids infamously went and changed the Aesop of the Pokémon: The First Movie as well as some of the character of Mewtwo. The original Japanese version was about Mewtwo trying to find his purpose of life and the Aesop was that Clones Are People, Too. As Warner Bros. didn't want a villain who was "morally ambiguous", 4Kids changed the Aesop to the less complicated "fighting is bad" (Now remember, this is a series that makes its money off of things fighting) and made Mewtwo into more of a villain that wants to destroy all humans and Pokémon unlike the original version. In the English dub, it keeps him wanting to discover what his purpose is. He destroys the lab he was created in because he felt that the scientists that created saw him as just a lab experiment that cared nothing about him. He decides to want to destroy all humans and Pokémon and exist only with clones after Giovanni reveals that he was just using him as a tool for the goals of Team Rocket and telling him that his purpose was just to serve him. Thankfully, the remake is Truer to the Text to the Japanese dub.
Multiple casual references to God, heaven, and hell were censored in the English dub or replaced with euphemisms.
The infamous episode "Love, Petalburg Style" episode had its plot censored in the English dub. In Japan the episode is about the characters falsely believing May's dad Norman is having an affair with a Nurse Joy. In the dub this plot point is downplayed, having them instead believe that Norman just had a fight with his wife.
Two scenes of Misty slapping Ash were removed in the dub. In the first episode you can still see Ash's cheek being red afterwards despite the edit.
An unintentional inversion occurs in the episode Beauty and the Beach, when an old man stares at Misty, his dialogue is about waiting a few more years in Japan, while 4Kids made it about... his granddaughter. But he still blushes and grins pervertedly.
An interesting, more recent case not done by 4Kids, but by The Pokémon Company International. The episode "The Whistle Stop" featured mumbling by James (inside his Victreebel) that, when played backwards, said "Leo Burnett and 4Kids are the devil, Leo Burnett!" This was an intentional easter egg made by Eric Stuart in response to being poorly paid for his commercial worknote Leo Burnett was an advertising executive. The most recent releases of this episode, such as the 2015 Johto Journeys DVD and the Pokémon TV app, replace this with audio of James screaming. It's a case of a dub being dubbed over. The original version still aired on Boomerang before Turner lost the airing rights to the show in early 2017, and Disney XD's print of the episode (released on VOD services) is the edited version.
A bit of censorship original to dub: the original version of the song "What Kind of Pokémon Are You?" contains the lyrics "Good luck with Muk and its Poison Gas / Make one wrong move, and it'll kick your Grass". Apparently due to complaints, later broadcasts of the episode (including the DVD release) replace this with a second line about Dratini and the Dragon type.
Post-4Kids Edits:
"Dawn of a Royal Day" is a Prince and Pauper story where Dawn switches places with her Identical Stranger, Princess Salvia. When the two switch clothes, the princess blushes and comments in the English dub that Dawn's clothes are "a little less than regal". In the original, she uses no euphemisms and complains about having to wear Dawn's short skirt.
The XYZ episode "Coming Apart at the Dreams" was partially reanimated for the dub, likely so that the Crucified Hero Shot of Ash and his Pokémon would lack any religious undertones.
In the twelfth episode of the Sun & Moon series, Meowth sees Mimikyu without its costume. Cut to Jessie & James finding Meowth's dead corpse floating in the water, and later his spirit getting put back in his body. This was removed in the dub.
In the sixth episode of Sun & Moon, Ash eats a disgusting meal he attempted to copy off a cooking show. In the Japanese version, he ends up vomiting sparkles all over Pikachu, who reflexively electrifies Ash as a result. In the dub, the implication that Ash throws up is still there, with the audio of the vomit remaining intact but the next shot of the house is extended, turning it into a Vomit Discretion Shot after all.
In "Alola, Kanto", a shot of the adults holding mugs of an unknown orange drink was altered so that the mugs would be holding green liquid instead.
In "The Professors' New Adventure", a close up shot of Kukui and Burnett drinking together at their wedding is redrawn so that the wine glasses they're holding become standard glasses.
During the Malie City gym challenge in "Aiming For the Top," the wrecking ball on the obstacle course and some shuriken being thrown at targets were redone to be pink and their SFX made more cartoonish and rubbery; with the latter featuring suction cups. Arguably, this makes some of the scenes funnier with Lillie completely missing the targets and almost hitting Ash, Kiawe and the Rotom Pokédex.
One scene had Crystal's mom slapping her. To avoid any vague implications of child abuse, the English version has her glaring instead. It doesn't make too much sense in context and the characters still behave like something more severe occurred.
The running gag of Emerald peeing in inappropriate times and places is censored in the Viz release.
A Crucified Hero Shot of the Unovan Gym Leaders tied up on crosses was censored to have them tied to poles instead.
Other:
The Viz translation of The Electric Tale of Pikachu was rife with this sort of thing, mostly because the original manga was filled with Fanservice up the wazoo (to the point where even in Japan it was censored between the original magazine release and volume release by mangaka Toshihiro Ono, who normally does hentai). It was a case of Tropes Are Not Bad, though, as most of the fanservice was geared towards twelve-year old Misty, along with the ridiculously large boobs Jessie had.
The move "Night Slash" is known as "Tsujigiri" in Japan, which literally means "Crossroad Killing" as a reference to the procedure of the same name where certain samurai would've tested their new blade or fighting technique by attacking a defenseless passerby, usually at a crossroad at night.
