Anti-Climax Boss: The Neukhia in the second part of "A request" . It deals even less damage than the proceeding boss (who is to be fair, That One Boss). Even though it sets it's self up as a puzzle boss (you have to hit 4 switchs around the map to damage it) it's really pretty easy to steal his flunkies' Genji armlets and pound it into the ground without using the weapon.
The Final Watch at the top of the third Brightmoon Tor. After facing off against wave after wave of brutal foes that can easily massacre unprepared parties many times over, your final foe is...an ordinary Crushatrice with only two Blackwind guards. The former does have more health than anything else in the game, but not a single Turning ability, meaning it should barely scratch you compared to the preceding fights.
Dreamhares and their cousins, Hoppy Bunnies exist to turn moderately challenging situations into teeth-grinding nuisances. They are extremely fast, difficult to hit and love spamming haste on their allies, or slow on your party. Dreamhares also have a highly effective charm spell to top it off.
Malboros also appear in several varieties, including a type that can Charm half your team without fail, whilst being immune to all status effects itself.
Also, anything able to attack you at extremely long range (looking at YOU, enemy Fusiliers/Cannoneers/Tricksters)
Facing large numbers of Fairies in small battle fields will result in "Slow" purgatory, even if you are 10 times their level.
Scrappy Level: The "An Earnest..." missions, which require you to find up to four dates for a chronically overscheduled petitioner. Amazingly, the lucky ladies care more about level, MVP trophies and other unspecified attributes than little things like gender and species.
Even worse with these missions is the fact that "An Earnest Delight" (the last of them) is PHYSICALLY IMPOSSIBLE to complete without dispatching, so if you are mainly using story characters then my friend you are FUCKED.
Once the player has completed all 300 missions, one final tournament becomes available. The first two fights are challenging. The third one consists of a pair of Tonberries, some enemies to cast haste on the Tonberries, and about four rounds of free turns for the enemies.
The "Time to Act" mission, which combines this with That One Boss, Luck-Based Mission AND Annoying Video Game Helper. You only have one controllable character, along with five guest moogle allies of various classes. If any one of the moogles is KO'd, you lose. How Scrappy the mission is mostly depends on the Tinker. If the Tinker skills go your way, the mission isn't so bad. If it ends up casting Haste on the enemies, you might as well turn off the DS and try again. What's more, the mission starts with an enemy Sniper packing the double-shot ability with a very squishy Black Mage moogle already in range, so it is not uncommon to fail this mission before your character even gets a turn.
Also a Guide Dang It, as it's never made explicit that the repeatable prerequisite mission to Time To Act increases the capabilities of the ally moogles in Time To Act.
Specifically certain laws that you may end up violating by an unavoidable accident. Namely "no damage above X, no hitting enemies more than 1 square away, or no critical hits" which you will end up breaking if you accidentally score a Critical Hit because you'll deal more damage than you expected to, will knock the opponent away counting the attack as damaging multiple squares away, or break the law for the Critical itself. Or the No Knockbacks law. Or the No Solitude law, if that was the only character next to you.
Many battles have enemies that are scripted to have one or two turns right at the beginning of the battle. Brightmoon Tor has enemies that cast Haste on themselves, doubling the number. One battle combines this with an Escort Mission to create one of the most insulting luck-based missions in video game history.
Tear Jerker There is a quest where you have to fetch someone zombie powder to end their life, and thus, their pain. All through this quest, this song is playing, making the burden the player takes on this quest far heavier, and the mood very sad. You do have the option of getting the memory-erasing herb so they can forget their pain, but the fact you have to make the choice between the request and what looks like the better option still looks tough.
What's even worse about this? The person wants to end their life with Zombie Powder to forget their pain. However, the Witch Of The Fens tells you that Zombie Powder preserves the user's memories. If you fulfill the request, the man is doomed to become a living corpse. Near-immortal, and still in pain.
Another quest is from a miner, requesting help in rescuing his fellows after an accident and talking of their cries in the dark. When you get there, the battle is against a number of ghosts. These are the miners, including the petitioner, who were unable to escape in time.
That One Boss: Lord of the Flowsand has a nasty habit of tripping players up, given how early it appears in the storyline. It has about 5 times the HP your characters do, capable of dealing high damage, has an attack that drains HP to heal itself, and to top it all off, it regenerates a percentage of any damage you deal to it.
The first fight against Illua isn't a picnic either if you haven't spent time doing sidequests. While you only have to defeat the Mark, her allies are hardly pushovers, and she uses unique and devastating magic that can quickly tear about your forces. How badly? Try 75% of all units' HP in 3x3 diamond. Illua also boasts high hp and the "Reflex" R-ability that allows her to avoid most physical attacks. Oh, and she also seals the Judge, meaning no clan privileges and no bringing KO'ed units back. Finally, beating her immediately sends your party into anotherBoss Battle without a chance to save in between.
That is, your judge gets sealed unless you do a ridiculously obscure and completely disjointed side-quest to prevent it.
Woolseyism: The Yojimbo class, meaning a samurai/ronin hired to be a bodyguard, is changed to Parivir, Sanskrit for bodyguard. The change is of questionable quality as the Parivir is a samurai class. To be fair, Yojimbo also means bodyguard.