Author's Saving Throw: Square Enix wanted to make games for the Gameboy Advance. Nintendo president Hiroshi Yamauchi, still bitter that they abandoned their company after Final Fantasy VI to make games for Sony systems and a rival portable console, wouldn't let them. What was SE to do? Create a special development contract that required them to create at least one GameCube game with a certain amount of sales profit going directly to Nintendo before being allowed to develop on the GBA. And the name of that GameCube-specific title was...
Game Breaker: The Cure Ring, or any other Magic Ring, as they can make it to where you don't need magicites anymore. The Cure Ring can make food items nearly moot.
Nightmare Fuel: Tida. It's a ghost town covered in fog, insect silk, Carrion Worms, and skeletons. All of its signs are notices for preparing for the Crystal Festival and welcoming their caravan home, after the opening cutscene noting the caravan failed.
The fact that so many people lose their memories. This can happen to the player character in the endgame.
Scrappy Mechanic: When playing multiplayer, instead of having a moogle carry the chalice for you, a player has to do it. This renders the player unable of doing anything but moving until they drop the chalice. And their movement speed drops.
The moogle isn't exactly safe from this either. After spending some time in a level, the moogle will get tired and complain, asking you to carry the chalice instead. When this happens, the moogle's speed noticeably drops, and your character will outrun the moogle, causing him or her to run headlong into the miasma. This means you have to let the moogle drop the chalice for a bit and waste your time, or carry it around (which leads right into said problems above) and be prepared to drop it again when you come across enemies. And when it says it is ready to carry it again, giving it back to the moogle right then and there will only cause it to tire out again not even thirty or so seconds later. Worse is if you go into certain areas without altering your moogle's current fur (you'll need to shave it if you plan on heading out to Lynari Desert or Mount Kilanda, and you'll have to grow it back out for some of the chillier areas like Selepation Cave), he'll tire out MUCH quicker. Granted, it's not exactly the most annoying aspect of the game, but it sometimes get irritating.
It should be noted that the moogle usually only has to drop the chalice for about five seconds before he's ready to carry it again.
This is particularly irritating if you're in the stage's boss fight, which can take quite a while on single-player.
Squick: Apparently, when you forget something, it's because Lady Mio 'nibbles' on your memories.
Superlative Dubbing: The only voice actor in the game is the narrator, but she still pulls out some very well-acted narrations (and of course, has an Irish accent to fit the game's Celtic theme.) Her singing voice is pretty good, too.
Tear Jerker: The games are adorable, the characters quirky and endearing... but the writers have a terrible fondness of killing everyone you love, and some people you don't. Frequently.
That One Level: Conall Curach is incredibly annoying due to being ridiculously large maze crammed with dead ends, and having pretty much the same scenery throughout, meaning you have no idea if you've taken a wrong turn along the way or not. Not to mention the majority of enemies there are Demonic Spiders.
That One Boss: The Dragon Zombie, especially on cycles two and three. His arena is incredibly small so it's very difficult to maneuver around and his minions are Stone Sahagins which take forever to kill.