Dawson Casting: Haley Joel Osment, Hayden Panettiere and David Gallagher have become this in the course of production. When the first Kingdom Hearts came out, they were 14, 13 and 17 respectively, playing characters who were 14, 14, and 15 respectively. However, by the time Dream Drop Distance came out, ten years had passed in real life while only two have passed in-universe.
Defictionalization: Master Swordsmith and Renowned Propmaster Tony Swatton made a Real-Life Replica of the Kingdom Key Keyblade after receiving a lot of requests from fans. No joke.
Fan Nickname: Apparently Luxord's is George Michael for the (unintentional?) resemblance.
Flip Flop of God: Though some of this is also the fault of Word of Dante, there's been conflicting reasons for why Sora and Roxas are able to dual-wield Keyblades. The current official explanation is that it's because he has Ven's heart inside him, and Roxas is able to do so because he's Sora's Nobody. This is a direct flip of what fans had previously assumed—that Sora got the power from absorbing Roxas, and Roxas in turn got the power from absorbing Xion.
In Re: Chain of Memories, Kairi and Namine, who are essentially two halves of the same whole, are voiced by Alyson Stoner and Meghan Jette Martin respectively. Those two also played archenemies in a rather popular movie. Make of that what you will. Doubles as The Other Darrin below.
Megara is a Pokémon trainer whose closest friend is Vivi. In Sinnoh, Aqua is a companion, and in Unova, Riku as well, while Sora is a stern champion with a Throh, and Roxas/Ventus is an annoying rival who somehow manages to win the Unova league.
Donald's got a role in each film: first, a mysterious fetus-looking creature seeking to destroy all clones, then a water god who chose Ash to bring peace, then a butler to the father of a creepy girl, then a hunter, then a chariot racer, then an ex-Team Magma member, then a professor who named Deoxys, then a legendary hero, then a Pokémon Ranger, then a cowardly baron, then a scientist who's spent five years studying Giratina, then a maniac bent on killing Arceus Himself, then a kidnapper who works for a seers, then a mayor, then a four-legged Musketeer, then the red leader of the Genesect Army.
No Export for You: Kingdom Hearts owns this trope (unfortunately). Neither Americans nor Europeans got their hands on Kingdom Hearts: Final Mix or Kingdom Hearts 2: Final Mix+, making everyone mad and further mucking up the narrative.
It looked like the latest installment to the series, Coded would go the same way until it was announced in E3 2010 that the game would be remade for the DS as re:Coded and released to Western audiences.
Which was quickly countered by Birth By Sleep: Final Mix, with Nomura being evasive when asked of a release outside of Japan.
This trope has finally been averted for all the Japanese-only updates, as the 1.5 HD Remix compilation release for PS3 contains Kingdom Hearts: Final Mix, along with re:Chain of Memories and cutscenes of 358/2 Days, and the upcoming 2.5 HD Remix will feature Kingdom Hearts 2: Final Mix, Birth By Sleep: Final Mix, and the re:Coded cutscenes.
The Other Darrin: Quite a few. A bad example being Mandy Moore replaced by the absolutely wooden Mena Suvari. A good example would be Lance Bass being replaced by George Newbern (who made it clear that the line is "Descend, Heartless Angel", not "Sin Harvest" as Bass' rushed delivery had many believing, including Dan Birlew, author of the official strategy guide.)
Corey Burton is The Other Darrin to a few of characters, most notably DiZ. He played MCP and Sark in II, although the original actor did want to come back but had schedule conflicts.
Geoffrey Rush, Captain Barbossa's actor in the movies, wasn't able to initially reprise his role in the second game.
Kairi's usual actress, Hayden Panettiere, is then the Darrin for Stoner's Xion in 3D.
Schedule Slip: Yoko Shimomura apparently has habitual problems producing her music on time. This got a whole lot worse during production for the handheld trilogy (coded, 358/2 Days, and Birth by Sleep), during which she was also composing for Final Fantasy XV, leading to Tsuyoshi Sekito and Takeharu Ishimoto composing a good deal of Birth By Sleep's music.
The game was originally supposed to be Mickey-themed, but there was a disagreement on whether Mickey or Donald should be the protagonist. They eventually decided to Take a Third Option and feature an original character as the protagonist.
Chernabog was to have been the original Big Bad, the embodiment of all darkness, taking inspiration from American Gods with the final battle being a gradual climb up the slopes of Bald Mountain to fight him. He was turned into a surprise boss from console limitations and Executive Meddling.
The final battle with Xemnas in KH2 was supposed be quite different, with Xemnas melding into a giant Transformer-esque creature◊ after absorbing power from Kingdom Hearts and, upon defeat, transform into this◊ distorted version. This idea was nixed and replaced with the dragon-fortress/armored Xemnas and black-and-white coat Xemnas battles.
Variants of Behemoths and Wyverns (from the first game) were included in the 1000 Heartless Battle in Kingdom Hearts II.
The Pridelands were originally going to be featured in the first game, but the engine couldn't handle the quadrupedal movement, so Simba was included as a summon instead. After changing the game engine, the world managed to make it into Kingdom Hearts II.
358/2 Days had a Pinnochio world which was Dummied Out. It would have included Gepetto, Foulfellow and Gideon, and Human!Pinocchio, and would have a What Measure Is a Non-Human?-centered plot and a focus on circus scenes. It was cut due to space limitations.
The outside walls of Hollow Bastion/Radiant Garden were originally going to be playable in Kingdom Hearts II.
An odd example is a scene from the Beta trailer of the first game, which has Riku at the top of Big Ben. What's odd is that, despite never appearing in the finished game, it is still referenced in later games as canon.
Both Hades and Megara were set to appear in 358/2 Days.
Rikku was originally supposed to have been with Leon, but the production team decided it'd be too confusing with Riku and Rikku, so she was replaced with Yuffie, who also got the outfit Rikku would have worn◊.
Vincent Valentine was planned to feature in the first game, but was replaced by Cloud, a more recognizable and iconic character.
A younger version of Irvine Kinneas was also supposed to be in Destiny Islands, but was replaced with Wakka (also more recognizable, although perhaps because of Kingdom Hearts).
Both Leon's and Cloud's pasts were going to be touched upon in Birth by Sleep, but as the world already had several members of Organization XIII appearing, it was decided that the world would have been too overloaded with characters.
Marluxia was originally envisioned as a woman, but was changed to a man because of the Unfortunate Implications of having two women attempt to overthrow a mostly male organization and falling flat.
The members of Organization XIII who died in Chain of Memories (Vexen, Lexaeus, Zexion, Larxene, and Marluxia) were going to be bosses in the Olympus Coliseum in KH2, but were cut. The Data-Battles of Final Mix are a remnant of this.