Game-Breaker: Hasten Time andO-Overdrive! The ultimate Hydrology spells, both achieved by Spell Synthesis (which can only be performed by Rosalian Mages and Imperial Scholars). Both allow you to instantly end the turn — for your enemies. Overdrive lets the caster then act five times, while Hasten Time lets the whole party get a move in.
Never Live It Down: In a sense; Galahad's mainly known for how you can kill him to get the Ice Sword. It's even better in the The Ultimania Story, he is killed then revived by Grey, Galahad even says: "You could have just asked me for the sword."
In order to unlock Jamil's best friend Dowd as a recruitable teammate in other scenarios, you have to play as Jamil, then let Dowd leave your party when he asks to stay in South Estamir. Later on, after agreeing to deal with the Assassin's Guild, you learn the hard way that he was kidnapped and brainwashed by said guild... when he's sent to murder Jamil while he's sleeping at the Inn. Said revelation comes too late to save his life. The Remake turns this into a full-fledged cutscene just to drive the point home.
Another potential punch doesn't need a cutscene: "Alright, I'll just pop into Weston real quick and WHAT THE HELL IS THAT THING?!" Note that this one can happen even if the player isn't aware of the Jewel Beast beforehand, making it an even worse shock for unwary players.
The fact the availability of events is based not in event flags or in-game time but in the amount of battles fought is perhaps the most baffling decision, especially given how difficult is to avoid fighting (see below). As such, you can find yourself missing several sidestories simply by deciding to grind for stats/money just to survive the Nintendo Hard nature of the game.
The weapon skill system in the SNES/SFC version. One learns new skills by leveling up weapon mastery. The issue is that the mastery is tied to that weapon in particular. Say, you want to upgrade your old iron sword for a new steel sword, then better be prepared to grind for mastery points to regain all the skills again. Minstrel Song thankfully did this away in lieu of a system more familiar to the people that played the newer games.
Field enemies in the SNES/SFC version as well. Somehow. Unlike most RPGs back then, the game features monsters on the field instead of Random Encounters. The problem is there are dozens of them per screen and avoiding them is nigh impossible given they're faster than you will ever be. It gets downright ridiculous in cramped spaces like tunnels and caves.
That One Boss: While most bosses can prove unpleasant if you discover too late you're unprepared, Flunky BossEwei is a particularly shining example. As are the Four Elemental Lords (and their Superpowered Evil Sides).
That One Level: The Isle of Evil. Features folding and moving stairs that accelerate the higher you climb; the slightest misstep sends you right to the bottom of the tower, forcing you to climb up again. Getting the timing right is... difficult. Oh, and if you leave, that's it: you can't come back. So you have to get everything done in a single trip.
That One Sidequest: In terms of getting the materials for it, Gray upgrading his Falcata is no easy feat, especially the specific type of Mullock needed to complete the quest, you just need to spam Blunt Strike many times in battle (Blunt Strike does no damage and may paralyze the enemy)
They Changed It, Now It Sucks!: Most of the characters got a new look for Minstrel Song. Not all of these makeovers went over well.
Viewer Gender Confusion: In Minstrel Song, Darque can fall into this, particularly due to their unique circumstances; Darque is male, but Aldora isn't.
