These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Demonic Spiders: Werewolves are the first enemies you encounter that can prove a bit challenging. Later enemies can also fall into this trope, depending on your gear, and your character's weapon/spell levels. The monsters in the Purelands hit quite hard if you forget to buy updated gear from Neko prior to heading there.
Most slimes qualify as they always inflict some status effect that's HP draining, payalyzing, or both. They also constantly respawn and are hardy creatures when first encountered.
Ear Worm: Much of the soundtrack is really pleasant to listen to.
Game Breaker: Casting the right offensive spells on a boss not only inflicts far more damage than any of your physical attacks, doing so also stuns it until the spell is finished casting, during which time you can cast another spell and so on until the fight's over. It's telling that That One Boss is the last one you fight without magic.
This works the same way when enemies cast spells on the player characters. Except the baddies don't do it every other second...
If you're lucky. The penultimate boss likes to SPAM YOU.
The iPhone port increased the aggression levels of all enemies and won't hesitate to combo and spam spells on you.
This gets taken Up to Eleven once you get Luna's magic: Not only can the Sprite spam-cast anything s/he wants, you can then drain the MP from the surrounding enemies to completely refill your reserves. Even the ones you just obliterated, if you're fast enough.
Good Bad Bugs: Using the Moogle Belt or the Imp Hammer causes you to remove or receive that condition, yes. That's not the bug, this is the bug: in between the three seconds it takes for the item to take it's effect you're invincible. Like, to, let us say, The final boss' charge attacks, effectively making him a lame duck except when he's in front of you (WHICH IS ALSO THE ONLY TIME YOU CAN ATTACK HIM) but his weak magical attacks make it impossible for him to kill you what with your overpowered player party and the cup of wishes, royal jellies, candies, chocolate bars and all the Undine Magic you have.
The man has some truly dick lines in the original-flavoured game - for example, taunting the heroes after dropping them into the room with the Chamber's Wall along the lines of 'oh, you can all freak out freely; after all, no one knows you're here'. And after all is said and done, and you've defeated the energy-slurping demon wall...? He calls you a second-rate/unimpressive Mana knight. Thanatos is a troll.
His response to Purim's freakout over his possessing her boyfriend is particularly bastardly, to wit: "Give Dyluck his body back!" "I am Dyluck."
Nightmare Fuel: A few kinds. Audio, in the form of The Curse (and Ceremony quickly turns into this given whom it becomes associated with over time); plot-wise, in the form of Geshtar the MechRider being turned somehow into a "living magical mechanism" (MechRider 3) by Thanatos - just what that entails and what actually took place in the process of this isn't detailed, but leaving it up to the player's imagination makes it so much worse; more plot with regard to why Thanatos has to pull Grand Theft Me every so often - Dyluck explains in the Japanese script that although your enemy's soul is indestructible, the bodies he takes over are definitely NOT, and they start to break down once he takes over - for a super colourful, adorable NES game, Secret of Mana is almost startlingly creepy when you think on it for a while.
Finding out that the main character's mother was the Mana Tree, and that his father was the ghost he saw after removing the sword. Then Thanatos destroys the tree.
Flammie's parents. Minor compared to the first one, but still caught you off guard.
Just about anything involving Purim and Dyluck, but especially Thanatos forcing Dyluck to kill her (she gets better, but still), and Dyluck's final fate.
Polished Port: The iOS version fixes some bugs and uses an interface designed to take advantage of a touch screen: instead of using an on-screen D-pad to navigate through menus, you just touch your choice as if it were a native iOS app. Sadly, multiplayer was cut, although there is always hope it will be added in an update.
Seinfeld Is Unfunny: Where to begin? First there's the unprecedented stunning visuals, the music, and the fact that a fair chunk of the game's plot was recycled by Final Fantasy VI, the fact that it pushed the hardware of the SNES to it's absolute limit... Let's just say everything that made this game great was quickly forgotten.
The "Action Grid" lets you program the combat AI of your party members. One of the first games to let you do this.
That One Boss: The Dark Lich is absurdly tough, even considering that he's the second-to-last boss. Don't attack him when just his hands stick out of the floor; it's done to bait the party, and he can get a Total Party Kill very easily if they hang around his hands. One of the only ways to win is to stunlock him with magic as long as possible, but this will leave you drained for the upcoming boss fight, with requires both Purim and Popoie to cast magic on Randi.
Spikey Tiger. Spikey was a serious pain, as it could cause immense damage, moved very quickly, and most of its attacks knocked you unconscious, leaving you unable to attack. It could also cast fire magic, against which there is no defense. And since this is the last boss you get before obtaining magic, you can only fight with your physical attacks when it jumps down to your level.
Lime Slime. It's friggin' huge, taking up most of the screen, and touching it hurt you; also, it had a pretty high magic defense, so your favored strategy of spell-spamming wouldn't be very effective.
Dread Slime too. As opposed to shrinking as it's health goes down, it instead just keeps growing and growing until it fills up the entire screen. By that time you'll be stuck between one of the crystals in the arena and Dread Slime itself. If you're very unlucky you'll be stuck far away from Dread Slime's weakpoint, so that you can only damage it with magic. If you run out of MP, you're screwed.
The Untwist: After learning that Randi removed the Mana Sword from the stone, Jema informs him that only The Chosen One should be able to do that. Jema tells you that since Randi is so young, it must be a mistake, and he was only able to remove the sword because the power of Mana had weakened. Guess what? Randi is the Chosen One due to his heroic parentage! Never saw that one coming!
Viewer Gender Confusion: The gender of the Sprite is a fiercely debated topic to this day. The English version says he's male, despite listing him as "The Heroine" in the manual, and it's even less clear in the original.
In the German translation, the Sprite is actually female and is referred to as "the little kobold girl" (die kleine Koboldin).
The JP version is - well, Japan has a lot of gender-neutral pronouns. The sprite uses 'oira' as a personal pronoun, and that one's usually used by guys... but tomboyish girl characters will use it as well so - yeah.
Popoie has no official gender in the original game, period. The JP guidebook lists the kid's gender as unknown.
Woolseyism: Understandable, since the poor guy had a month or so to translate the game and the programmers utterly refused to change the text's width or just couldn't, leaving him with not a lot of time and even less space. A fan romhack/retranslation restores the intended life to the script.
From Woolsey himself: "Probably 40 percent or more of the text was nuked - there just wasn't space. Story elements, nuance and personality had to be stripped out. It was, in some ways, the hardest game I'd worked on. I loved that game, but am probably most dissatisfied with the result. I was there for over a month, and the screen text was being modified every day. Certainly tried my best, but that thing nearly killed me."