The toy helicopter level in GTA Vice City. Brings the game to a grinding halt, and it controls like garbage.

Project IgI. If you don't get into some of the buildings, the enemies keep reproducing. It's should have a limit.

I'm surprised no one has mentioned the Triforce fetch quest in Wind Waker. Even when greatly reduced in WW:HD, it's still a drag and kills the momentum of an otherwise great game.

A very recent example: Rampage quests in Monster Hunter Rise. You can choose to not do any except for 2 (1 village and 1 hub) that are part of the progression as you increase in rank. I hate them in a game I honestly liked more than I thought I would.

Otherwise other examples are:
-Any ice level in Snake Rattle 'n Roll (NES)
-Motorbike level in Battle Toads (NES)
-Time/move limited missions in X-Com EU/EW
-Bosses you are meant to lose to in any game just instakills the game for me except when it is a opening fight where it is obvious you should get stomped and only hold out for a while before being stomped.
-Medusa heads in any classic castlevania :P

That helicopter mission in Vice City
The pilot school in San Andreas
That sniper mission on the boat of GTA 3

Sky Keep in Skyward Sword... definitely my least favorite dungeon in the game.
Dry Dry Ruins in Paper Mario... as far as desert areas go this one is pretty bland and the difficulty spike for this part of the game is actually quite high.
Silph Co in Pokemon FRLG... too many damn trainers, it takes so long to complete.
Formidable Oak in Pikmin 3... I dread playing this every playthrough.
Corona Mountain in Mario Sunshine... another area I dread playing.
The Cortana level in Halo 3... just fuck this level and fuck the Flood haha.

That's all that I can think of off the top of my head.

When I die in Returnal after what I thought was a pretty good and lengthy run... The redo everything from scratch aspect of Rogue lite/like/whatever-that-stupid-name-genre-is-supposed-to-be ruins the experience for me by having utterly no respect for my time. But I understand Housemarque’s desire to keep that arcade aspect of their pedigree intact for their first big budget game. Still not a fan. But the rest of the experience is excellent.

As a kid I used to hate the entire Maridia section in Super Metroid because I got lost so bad.

FF X - Bliztball 

Kingdom Hearts 1/2 - Spaceship sections between worlds 

Kingdom Hearts Birth By Sleep - The Ice Cream minigame in Disney world. Actually, all minigames in this world are annoying but Ice Cream is insufferable 

Fire Emblem Three Houses - Investigation quests in Garreg Mach 

Breath of the Wild- Any shrine where you have to use gyro aiming. If shrines still optional in BOTW 2 I will skip any section where I have to use this abomination 

Crash Bandicoot Warped - Any level you have to drive a motorcycle 

I don't know, that never bothered me at all, honestly. It gives you a nice opportunity to swipe one last time over the entire map and collect everything you still haven't yet to prepare yourself for the final area. The same in Metroid Prime.

¯_(ツ)_/¯