What are some portions of games that piss you off, despite you really loving the rest of the experience?

The Gerudo region in general is a drag to explore in Breath of the Wild, from the mountains to the desert itself. As such, it's the first one I always do in my playthroughs, so I can enjoy the best ones at the end.

Library. - Halo: Combat Evolved.
The Fade. - Dragon Age: Origins.
Water Temple. - Ocarina of Time.
Tutorials. - Every game ever.

Resident Evil 4 - the island. Not sure how I love this game so much, considering how much of the island I hate. Particularly everything from the Krauser knife / boss fight up through the two rooms after where the helicopter helps you clear out the waves of enemies. The boss in the cage is the only bit that comes to mind that I like.

Twilight Princess - that temple in the Sky.

Super Mario Sunshine - that Watermelon Festival. And Eely Mouth Dentist. I dread both every time.

Tomb Raider III - I really enjoy this game, but there's so many sections that are torture that I'm not sure where to begin. Madubu Gorge and a lot of London immediately spring to mind.

Banjo Kazooie - Rusty Bucket Bay. Guaranteed to die and lose all my notes.

Epidemics in Theme Hospital.

The Fade Dragon Age Origins
Mission 11 Devil May Cry 4
Mementos Persona 5
Stealth Mission for Warehouse Shenmue
Defend Train, Daemon X Machina
Darksiders II Caldrun
Final Fantasy IX Cid sneaking/Card Game
MJ Sections Spiderman PS4
Text Adventure section in Nier.
Red Giga Fight, Skies of Arcadia

Bosses that throw generic enemies into the mix mid battle. It really annoys me having to pick off the grunts whilst trying to avoid a bosses attack, and memorise its patterns. This is coming off the back of an enjoyable playthrough of journey to the savage planet, which was slightly hindered by the bosses.

Pretty much any retro RPG where you have to grind. I have always hated grinding so much. I remember playing Dragon Warrior a few years back on my NES (it was a bucket list thing) and literally feeling as if I was going to lose my freakin' mind.

Ordon Village in Twilight Princess.
The plot stuff is fine, but spending an hour in what are effectively tutorials was not my cup of tea. Thankfully I got out into the real game before my interest waned too much.