From what I hear, Final Fantasy 10 has one particular boss fight that's like this. Specifically:
* There's a 5 minute cutscene before the boss fight, that you need to watch every attempt.
* The boss fight has 3 phases.
* The second phase uses an attack that infects Zombie status on the entire party. A typical player, on their first attempt, will likely want to cure the status ailment, since it prevents you from healing the affected characters.
* The third phase opens with the boss using an attack that instantly kills everyone who isn't under Zombie status. If the player has been diligent in curing Zombie, then this will be a game over, forcing the player to re-watch the cutscene and replay the fight from the beginning.

Final Fantasy 10's post-game content, particularly the Dark Aeons and Penance, are also examples; here the problem is that the boss fights are long and boring. (That one other boss I mentioned is at least interesting other than the forced cutscene and the sudden death in the final phase.)

Other examples:
* FF5 has a superboss in a chest, some distance from a save point, that will wipe your party if you're not prepared (~8000 damage to the whole party when fighter-types "only" have HP in the 3000s).
* I've heard terrible things about Digital Devil Saga's superboss.
* SaGa 2, a game where attack magic is normally quite useful as a primary means of offense and where using an attack type makes some characters better at it, throws a boss that's immune to the damage spells available at the time, and status ailments are less reliable than in other SaGas.
* Paladin's Quest's final boss is also unfair.

(I don't have time to elaborate now, but maybe later I will.)

Yeah also missions where you HAVE TO keep someone alive or Mission failed FFS SO INFURIATING!

I stand by my statement that FFX is best enjoyed with the non-"International" version that doesn't have the Dark Aeons.

Well, I'm not sure... the whole thing seems half-baked to me, so to speak. The game is quite short and feels under-developed, like they ran out of budget halfway through, or something like that. The very feature that should give the game its uniqueness, namely, the ability to morph water, comes into play only near the end and has a marginal role altogether. Yet, as I said, the game is short so maybe you could give it another chance after all. But beware, if you manage to reach the end, you're in for a world of hurt (unless you're much more skilled than me at playing videogames, which might very well be).

oh please, that section is an absolute doddle.

I nominate Mortal Kombat. Those final bosses are so painful to do. What Crosmando says. The game is beautiful and well made but the gameplay and level design it just tedious and irritating. I couldn't have felt more disappointed with that game. I adored Doom 2016.

Paladin's Quest's final boss:
* Is much stronger than anything else in the game
* The boss can be particularly dangerous, with two actions per round; it's quite possible that the boss can take you down from full HP to dead in a single round, and there are no mid-battle revives.
* Only one of your characters can do meaningful damage, and doing so costs 250 HP. (You might typically end up with around 1500 on him by end game.)
* Is actually the second part of a compound boss (the first part is not so bad), which is at the end of a fairly long trek (though at least you get a bottle refill shortly before the final boss).

The only saving grace here is the Gigabl item; there are 2 of them, there are 2 characters who can equip them, and each one has 9 uses (refillable, but obviously not in the middle of the boss fight); when used, it fully restores the HP of every living party member. Unfortunately, one of them is permanently missable (one of the worst missables I've seen in an RPG).

(Lennus 2's final boss, on the other hand, is perhaps too easy; the game even gives you a mid-battle full revive, but in practice you don't actually need it here.)

I'm gonna shotgun this a bit:

Bosses you're supposed to lose against but aren't told or indicated of.

So much this.

A very large name game that I played recently had a bit toward the end where you were expected to lose the fight. I hung on for a solid 30m until I finally looked up a Youtube video that hinted that I should have lost.

Unless it's obvious, like if all your attacks miss or the boss suddenly uses an attacks that wipes out your entire party in one hit.

Dragon Warrior 7 is one offender here, as there's one boss that feels like it should be killable (the only clue is the boss using a spell that's strong for that point in the game, but not overly so), but in actuality it has something like 65k HP (and might even regenerate about 100 each round, as some DQ bosses tend to do).

In Lufia: The Legend Returns, there's one boss in particular that you're not supposed to kill, but that fact isn't obvious, and there's a good chance that a first time player will actually defeat that boss. Fortunately, the game actually does something interesting; if you manage to defeat a boss of this sort, you get a special item as a reward.

On the other hand, the very first boss of Lufia: TLR is a pain if you want to kill it (it's another "supposed to lose" fight). The strategy requires gathering a bunch of Hi-Bombs (which are rare at this point), and even once you have them, you need to hope the RNG is in your favor, as you need lucky damage rolls to win. Plus, retrying is a pain, as you have to go back through the dungeon each time, and have to sit through the "THIS is what I call frue [sic] descruction" line each time.

(I'm not sure if you can get those treasures if you miss them, but I *think* they appear randomly as blue chest items in the Ancient Cave, which is one of the most interesting and unique minigames I've seen (even if it is taken from Lufia 2).)

I really really hated the last boss of Ys 1. You can't avoid his attacks and win by playing defensively because he simply removes the ground under your feet. He's fast, bounces like a rubber ball and your only option is to take a lot of hits and try not to stay exactly where he will open a hole. You can't even stand still waiting for his path to come close to you.

What's even worse, you might follow everything I said and still reach an unwinnable state because as he removes ground he can divide the platform in two and isolate you in a small section, thus granting he can bounce around most of the screen shooting at you with no danger to himself.

Don't forget that the strongest weapon in the game (in terms of attack power) does not work well against this boss, and you need to use a weaker weapon if you want to be able to do enough damage. (If you try to use the strongest weapon, your attacks won't do enough damage to kill the boss before there's nowhere to stand.)

I should also point out that the boss only destroys the floor when you attack it.

Personally, I don't mind that boss as much as that one bat boss in the middle of the game, which practically demands that you max your level (even speedruns do that!) and is extremely RNG dependent. The boss can just stay in bat form indefinitely, and there's no way to hurt the boss when it's in that form. Then the boss forms into its humanoid form, and you have less than a second (IIRC) to get a hit on the boss. What's worse is that sometimes the boss will look like it's about to change into humanoid form, but then immediately expand again without doing so. Basically, the boss is only vulnerable when it decides to be. (Worth noting: A TAS of the boss rush mode deliberately took extra time on the previous battle just to get the RNG into a favorable state for this battle.)

The bat boss appears again in Ys Origin, but is a much more reasonable fight; the time the boss spends in boss form feels like it's reasonably bounded, and the boss stays vulnerable long enough for it to launch a projectile attack. (Ys Origin has many bosses from Ys 1 and 2 in it, but there's always new twists thrown in to make the boss feel fresh, and this boss is no exception.)

Back when they made Ys 1, I think Falcom didn't yet know how to do good boss fights.

By the way, in Ys 2, the last two bosses require you to spend time leveling up before you can defeat them; if you do not, it is impossible to damage the boss. Furthermore, simply killing every enemy you see won't get you enough XP; you have to spend extra time earning XP before you can damage the boss. (You also see this in Crystalis (NES, not GBC interestingly enough) and in the Famicom version of Ys 3.)

I could also mention some early RPG bosses that had full heal spells; you see this in Dragon Quest 2, Final Fantasy, SaGa 1, and the NES adaptation of The Bard's Tale.

https://snk.fandom.com/wiki/SNK_Boss_Syndrome

I forgot about most of those final battle details. Shows how much I hated it.

Curiously I didn't have a problem with the bat boss. I even remember having to reload an earlier save and defeat him a second time and I still had an easy time against him. Maybe I happened to come across a favorable RNG state by pure chance.

As for later games I can't comment on them because I stopped early in Ys 2 and didn't even buy Origins yet. It's not like I'm too eager to pick it up anyway.

Verminator from Secret of Evermore.

Huge rat guy who's stood on a raised platform of boxes so you can't hit him with your weapon, and he can fling random stuff at you with impunity.
The only way you can do anything to him is with alchemy; the game's stand-in for magic.
And it's entirely possible that by the time you get into this fight you've done absolutely nothing with alchemy at all beyond basic healing, as there's not really any need to.
So you get to "fight" a boss you can't even hurt for a few minutes before you get your face pushed in.

If you know it's coming you can prepare for it. But going into this blind your first time can be incredibly frustrating.

It's been a long time since I've played that game, but can't you used ranged attacks, like fully charged spear attacks?