The sequel leans in a different emotional direction in my opinion but the original Pathologic absolutely has a lot stuff that provokes an exasperated anger at the town and it's inhabitants.

In mm battle network 3's postgame, bubbleman v3 is a coward and will only reencounter you if your health is below 20% or so

Minor example, but Kid Icarus Uprising has one really long level with copy/paste arenas and hallways everywhere and the characters constantly complain about it not being over yet, lol

There's a platforming minigame in Danganronpa V3 that feels awful to play, but it also meant to convey the hopelessness of attempting to escape

In The Last Guardian, Trico is purposefully designed to disobey commands, make solving certain puzzles tedious, and even hurt you or get you killed to convey that this is a giant man-eating beast that you can't control so much as learn to work with. I think the player is supposed to be pissed off at Trico for a lot of the game until something clicks and they learn how to work with him/her.

^ Seconding this, The Last Guardian's a great example. Trico's occasional disobedience is one of my favourite parts about the game, it goes a long way toward making him feel like a real living creature rather than just some AI puppet.

TLG is a great example!

every lisa game (the first, the painful and the joyful) feature an area called "the meaning of live" thats just a long uneventful rope climb, generally about a minute and a half long, that at the ends with a big middle finger. you then have to climb the full length of the rope back down afterwards.

the world ends with you has a special pin that is particularly powerful once upgraded to its fifth stage and put in a set with the other stages. however, if you overlevel + overevolve it, it'll go right back to its first evolution stage (or in the japanese version, turn into... 1 yen.)

Genocide route in undertale maybe???

Forbidden Siren has some arcane requirements for progression, requiring you to piece together which characters need to pick up a specific item in a given level so that you can finally unlock the next stage. Suits the game well though- feels like you're trapped in the same purgatory as the characters.

TTYD's search for General White
Everhood has a secret ending locked behind a 1000-screen hallway. Around halfway through rocks start appearing that block you from just AFKing while holding right.
A lot of golden age point-and-clicks do this what feels like constantly, I'm blanking on specific instances right now though
Not a mechanic, but the zora king taking years to scoot over in Ocarina of Time will always be my favorite example of this

most of Cruelty Squad

If you haven't played it I can be more specific

a few come to mind with monster hunter...

in freedom unite, your felyne chefs who are meant to help you prepare for quests can easily give you food poisoning if you choose the wrong arbitrary ingredient combination. it also never records the effects of each ingredient combination, and these effects change wildly based on how many chefs you have.
also dung bombs seem to do little in this game other than fill the screen with brown haze and annoy your teammates. they can confuse khezus but otherwise it's difficult to tell if they actually can make monsters leave the area in this one (in later games they clearly have this effect).

also tri introduces deviljho as an aggressive invader species that can disrupt your quests. bazelguese is also designed to do this with bombs in mh world

another one (somewhat spoilery) but mask de smith in killer7 is intentionally the worst smith to use at the start of the game to emphasize the game-breaking buffs he gets later on, and to teach the player to mind when and where they reload

and in cave story, one of the ''''best'''' weapons, Nemesis, fires flamebolts normally but shoots harmless rubber ducks instead if you max out its level

AA2 also has that stupid circus case where you'll get penalties for pressing Moe on useless testimony because the judge is getting impatient. that same case also gives you a 50% penalty if you imply the judge might be responsible for the crime, with no warning.

And in Dynamite Headdy, two of the potential head upgrades you can get from the item roulette are useless. One puts you to sleep ala Kirby, the other weighs you down and halts you from all but a slow crawl

I don't know if it counts, but Castlevania II: Simon's Quest has a lot of NPCs that purposefully lie to the player to throw them off, while a few others have important information needed to progress the game (that is, if you're not using a guide).

Also, both The Witness and Braid have challenges made just to make fun of completionists by deliberately wasting their time. In Braid, that takes form of an optional collectable that can only be reached after waiting two real world hours for a cloud to move all across the map.
In The Witness, it's a hidden puzzle inside of a 56 minute long lecture about why you shouldn't hide secrets that is started at the beginning of the speech and can only be completed at the end. Pausing the game resets the video entirely.

One small correction: the game with the lying NPCs is not Castlevania III: Dracula's Curse, but its predecessor, Castlevania II: Simon's Quest (https://www.backloggd.com/games/castlevania-ii-simon-s-quest)

Cat Mario, the entire game was created to be frustating

pokemon platinum has that one npc that'll trade you a haunter with an everstone

Pokemon Channel.

Like, the whole thing.

You have to acquire 99 tofu for a trophy in Omori. You have to buy them one at a time.

would Drakengard count?

I think so! Everything I have heard about the game leads me to think so

if you want a certain level of a chip in battle network 4 you have to make sure you get it in that run. Other ways of getting it are playing through the game 3 times again or rng at a chip trader.

In the Monty Python's Holy Grail CD ROM point&click, when you reach the Black Knight you have to fight him to progress, it's very simple and almost impossible to lose.

HOWEVER, it also gives you the option to play as the Black Knight, a very long
tedious, sluggish and difficult fight viewed through a narrow helmet visor. If you manage to win, killing King Arthur, you get a game over screen and have to restart the game.

Not sure "pissed off" is the exact desired response, and some people (myself included) really loved it, but Arrest of a stone Buddha is designed to very heavily hammer home the hollow tedium of the hitman life. Also the folk expecting Ringo 2 were raging.

Sounds like Stone Buddha would qualify if you can give me a specific example!

The action stages of Stone Buddha are performed at a very slow walking speed, and enemies spawn infinitely until you reach the end. There's also no HUD elements at all, ammo and health and remaining distance are a complete mystery, impossible to tell which gunshot is going to kill you, and there's no checkpoints.

The city exploration stages have the same walking speed, and end only when you get home and take a sleeping pill, BUT you can run out of pills (again, no HUD) and the pharmacy closes at night. There's activities, but they're not any fun to perform, and most don't even pass the time any quicker.