Accidental Innuendo: "Guys, I gotta go inside Riku and take a look." "But who's to say it's even safe inside Riku!?" Hoo, boy.
Author's Saving Throw: In regards to its appearance in 2.5. The Days cutscene movie had drawn flak for not adapting the scenes in the Disney worlds, so this cinematic venture not only adapts them, but also includes brief battle scenes. Nomura himself admitted that the transition from pre-battle to post-battle cutscenes in the Days movie was awkward and rectified it here.
Captain Obvious Reveal: Data-Roxas being the hooded figure that appears before Sora in the endgame was a surprise in the original Re:coded, as the lack of voice clips or other overt clues kept their identity ambiguous before The Reveal. In the cinematic adaptation made for the II.5 Final ReMIX compilation, however, the figure is instantly recognizable since there is no attempt to disguise Jesse McCartney's voice, and is played less as a twist—there are several scenes where Roxas's face is visible while his hood is still up.
Some of the random Balloon Letters you can get can be this, at least if you get all the jokes and references. Just see for yourselves.
Jafar and Maleficent both getting confused by technology jargon. Jafar thinks Pete's "Galiches" (glitches) are some form of sorcery, and Maleficent mishears datascape as "date escape."
Demonic Spiders: The block spider heartless that you encounter in Data-Riku, see the entry for Kingdom Hearts on this trope's article for more information.
Disappointing Last Level: The game essentially ends with you playing an hour of Chain of Memories. Vibrant interesting environments are replaced with pathetically easy single room puzzles, most of which consist of speaking to the right NPCs in the right order. On the other hand, this segment is incredibly psychological, and for some, it's the best part of the game. And the boss fight against Data-Roxas is worth it.
Judgment Triad in the remake. FULL STOP. It can hit air enemies easily, has homing capabilities, is easy to aim, can hit multiple enemies, and worst of all, does such insanely high damage that almost every enemy, including most bosses, will be one-shotted by it (and the one that isn't one-shotted will at most take 3 shots to bring down). It makes even the Bonus Boss battle just all about dodging with the dodge roll, and aiming Judgment Triad. AND you can have four in your deck. The main downside is that you won't be able to have anything else in your deck, but who cares?
Below the broken Judgment Triad is Triple Pursuit, which while not as ridiculous, is quite insane. It is a tracking Ice elemental attack that does good damage and lasts extremely long, to deal multiple hits and freeze enemies that aren't immune to it almost every time. Its ingredients? Two commands that you can buy (or get) relatively easily because one is a Basic Magic command and the other can be bought right after you complete the fourth world (and it costs a mere 12,000 munny). Easily a Disc One Nuke.
The 30 layer labyrinth in Olympus Coliseum has powerful enemies in large numbers on lower layers. The going becomes a lot easier with Tornado Tracer. It becomes the command Breath of Zeus L2, doing high damage to all enemies for one command. Whatever isn't killed is easy to mop up with normal attacks from Hercules and Cloud. The only catch it that the ingredients to synthesize it are a bit pricy (Aero Edge + Cure, Stop, Slow or Aero to make Aerora, then Aerora + Wind Dash or Wind Tracer, total of 4,400 munny).
Forget commands, the most broken ability in the game is Targeting Scope. The last ability on the 0/1 keyblade, it makes your basic attack automatically strike the nearest enemy, regardless of distance. Walk into a room of Elite Mooks, swing for five seconds, and everything dies. The best part? One of the earlier clock abilities makes every. Single. Attack. A critical hit. It's easily in the same league as Judgement Triad.
Genius Bonus: The Metal Chocobo upgrades are all named after the chemical symbols for various "metals": Fe for iron, Ag for silver, Au for gold, and Pt for platinum.
In Agrabah, Data-Sora wonders why the town is so quiet, indirectly lampshading the series' lack of generic NPCs.
Data-Sora has to collect Inklings to help restore characters' memories.
Moral Event Horizon: Pete attempting to crush Donald and Goofy to death in Bug Blox in Hollow Bastion with absolutely no remorse and enjoying himself in the process. Thankfully Data-Sora reclaims his Keyblade and Mickey shows up too.
Narm: The script's insistence on using the word "hurt" as a noun (instead of using the occasional synonym, like "pain") is pretty awkward, especially in Castle Oblivion. The use of "hurts" as a plural noun ("there are more hurts than the one you have just undone") is particularly clumsy.
Nightmare Retardant: Unfortunately, all that happens when you run out of time is... you go back to the beginning of the area. With a full time gauge, no horrifying death animation, or even a Game Over screen. Regardless, it's still one of the most disturbing scenes in the Kingdom Hearts series.
There's something extremely unnerving about going through the worlds in Castle Oblivion, with everyone—or at least their illusions—acting as though things are totally normal, not knowing that what they're seeing isn't real... The melancholy music doesn't help either, especially since it puts you in the frame of mind to imagine all sorts of depressing interpretations of the alternate endings..
The SP wager for System Challenges is not optional, forcing you to pay 10% of whatever points you have if you feel like the challenge is too hard to do. This is particularly annoying if the challenge is "Play at night!" because you can't even attempt it; you either have to wait until it's night time according to your DS Clock or just suck it up and take the penalty.
If a System Sector floor has a virus, you're forced to wager all of your current SP for the System Challenge. This is just unfair because the game doesn't warn you until you're on the virus-infected floor, and if you're not prepared to do the challenge and fail the lack of SP will force you to do the System Sector again to have enough SP to buy anything.
The conversation with Data-Namine at the end of the game was for a long time the only part of the story anyone cared about, as it's (1) the only part of (the original version of) the game with any direct connections to the Myth Arc and (2) it's where "Sora" finally gets to thank "Namine".
Tear Jerker: Despite this being a relatively lighthearted game in the series, the moment Data-Sora discovered Xion's existence and her fate is strangely poignant.
Data-Roxas is hands down miserable. The poor kid not only has to deal with the non-existence of being a Nobody, he's a DATA CLONE of a Nobody. Understandably he doesn't take it very well, and seeing how just plain bitter he's become is heart-wrenching.
In addition, he keeps mocking Data-Sora about forgetting the people he met every time he leaves a room in Castle Oblivion. Connect that with Xion's fate in 358/2 Days and that certainly leaves a whole new layer to his bitterness.
They Changed It, Now It Sucks: coded translates the new line in the Journal as the rather fancy "We must return to free them from their torment"; it was changed in Re:coded to the more straightforward "Their hurting will be mended when you return to end it"; another change is "Their torment has been lessened" to "There are more hurts than the one you have just undone". There are plenty of ways to argue as to which translation is "better".
Tough Act to Follow: As many reviews for the game have noted, following directly after Birth By Sleep doesn't do Re:Coded a lot of favors.