I'm going to be a bit more liberal with the word "love" and also include games I just really, really enjoyed. 

REmake 2 - Maybe it's better for Claire as I only played Leon A's playthrough, but almost everything after the final segment of RPD in this game is just boring and bland. It's so sad because the RPD section of REmake 2 is one of the best things of all of last gen, but the last 35% or so just showcases everything wrong with the game in one long stretch. The Mr. X scripted segments that aren't scary or intriguing at all, the story which gets worse to the point of being laughably cliche (I mean come on Ada), the lab puzzle where it was confusing what you were supposed to do and in what order. 

Paper Mario: The Origami King - The desert in this game is so bad it's crazy. The only good parts about it are the music in the city, the dungeon, and the tornado boss fight which seems like a lot, but it's also like a 2.5-3.5 hour segment of the game, given it's one of the major areas, and the actual desert itself is horrible. Ressurecting the towers is horrible, the AI companion is boring, the vehicle controls suck, and the desert is very bland with a lot of areas that amount to nothing. Really disappointing. 

Luigi's Mansion - Ok this is a little bit mean because it's up for debate if it's really a "section" of the game so much as a continuous gameplay element, but the backtracking in Luigi's Mansion sucks. It sucks so much that it almost makes me wonder how people can prefer the formula of 1 to 3, despite the mansion itself being pretty cool. There is pretty much never new revelations from backtracking. All the cues and inspiration Luigi's Mansion took from Resident Evil are skin deep and it ends up being super bland to backtrack because of that. Luigi stays the same slow ass speed even when the lights are on and he knows a room is cleared. You only open one shortcut in the entire game (aside from the mirror trick, which isn't even that helpful in backtracking most of the time because you can't transport back to where you were from the mirror in the main room). Keys are door specific instead of a few keys being usable for multiple doors, which means you always get a notification on where to go every time you pick up a key, not only does this take any fun out of exploration but it means you're always forced to check the map to go to one specific point, and if you forget where to go you have to check because there's only one door where the key is useful. In general exploration in this game is kind of shit. 

Ace Attorney - Case 5 was added in the DS versions of Ace Attorney and kept in every subsequent re-release, it is not the actual ending to the original game. Yet despite never playing the original Ace Attorney till the Trilogy HD re-release on the Switch, I feel the way the story concludes with case 5 is super out of place. To be fair, I actually don't hate case 5 so it probably doesn't make sense to bring it up here, but I hated a lot of it - especially initially. It kind of redeems itself in the second half, but it's super long, and it makes the fatal mistake of kind of using the same exact set up as the legendary Case 4. It even sets up your partner to kind of be a replacement of Maya, only now instead of being kInDa quIrkY tHO bUt pSycHIC, she's KiNDa QuIRKy tHo BuT SciEncE gIRL. It's really annoying how similar the set up is to case 4, and a lot of the characters are a bit irritating initially, but again it is saved in the end, in large part because of the epicness that is GANT and the amazing security officer guy. 

Pikmin 3 Deluxe - The "puzzles" that involve using the 3 captains are mostly a waste of time and require no real micro-management whatsoever. 

Majora's Mask 3D - The Pirate Bay and the final dungeon are some of the worst parts of mainline Zelda ever, and that's really sad because this might just be my favorite and both hit you pretty close to each other. The Pirate Bay is pace breaking and just fucking dull and boring, not to mention it can be a little confusing on your first time. Plus the swimming controls suck, at least in the 3DS version. The final dungeon is fine at first but gets ruined by one weird jump that just seems like something Nintendo would normally never put into a game (?) and a map that's really bad for the type of dungeon it is - it doesn't change when you flip the dungeon upside down. Again, this is kind of a Super Metroid Maridia moment where aside from like 2 things it's pretty easy to navigate the dungeon, but those 2 things that are hard and confusing to find are necessary and it's just annoying that the map is so bad because of them.

Halo 3 - Cortana is one of the worst, if not the worst level, I've ever seen in a videogame. It's sad that the Halo game where Bungie finally made consistently great levels back to back had it's streak ruined by one level - not just any level but one of the most important from a story perspective and the second to last level in the game   . 

Nier Replicant’s Barren Temple.

Awful game/level design.

Water levels can be hit or miss for me. I'm generally not crazy about poison and darkness/torch levels, though.

That reminds me of the pure evil turret sections in Jak and Daxter 2 or maybe 3. The Dead space one was a cakewalk in comparison.

The imprisoned round 3 is where I gave up on Skyward sword (after already having quit before on the imprisoned, but came back later for the sand sea) The motion controls kept killing me, then you have to sit through all its cut scenes again, never again.

I also hated the sections where you play Ciri in TW3. Annoying invisible walls or instant death if you 'escape' and infinitely spawning enemies. Bad game design.

Good call!  Darkness/torch levels are even more annoying than water levels.  I love Dark Souls so much, but I really hate the darkness part.  

I can't think of any poison levels I've played through off the top of my head, but that does sound pretty sucky.

EDIT: Now that I think about it, I guess Dark Souls has a poison level too.  That makes me realize just how badly I hate the darkness level though, as it took a while for that poison level to register.

In no particular order (and sometimes stretching the definitions of "love" and "hate"):

• Age of Empires II - Some of the campaigns are better than others. The Saladin campaign, despite being presented as a moderately difficult one compared to the Ghengis Khan and Barbarossa campaigns, is pretty horrid due to a combination of challenging opponents, restrictive population and in-game tech limitations, the Saracens faction not having great bonuses to rely upon, etc. Some versions of AoE2 make certain sections easier, such as by increasing the population limit slightly, but will also make other sections harder, such as reshaping some geography to prevent cheesy tactics. This all culminates with a mission where you have to build a Wonder in a city while fending off attacks from 6 NPC players at once. And of course, Definitive Edition gives you an achievement for actually wiping out all 6 factions before beating the scenario.
• Doom - The entire fourth episode of Ultimate Doom is an unreasonable difficulty spike compared to the rest of the game, all while barely offering any cool ideas, mechanics, or enemies.
• Final Fantasy X - The Thunder Plains is a portion of the game with a gimmick. Lighting will randomly try to strike you and you will have a moment to dodge it, otherwise you get knocked on your feet and will slowly get back up. It could be worse... until you realize that you get rewards for dodging lightning enough times in a row. So the entire area ends up becoming all the normal challenge of a JRPG combined with random difficult QTE's mixed in whenever you're not in battle.
• Kingdom Hearts - Atlantica is one of the few worlds that appear in both of the major PS2 games. In each game, it is the worst area in the game.
• Legend of Zelda: Wind Waker - Who thought that making the first dungeon a stealth section was a good idea? For a game that promises the freedom to explore a vast world, it sure is quick to offer a slow and tedious section inside a few corridors.
• Paper Mario: Sticker Star - I'm apparently one of the few people who sincerely enjoyed this game, but I can't forgive how long and byzantine World 3 is. You have to go in and out of so many levels and figure out so many obtuse puzzles that many people probably never saw the more interesting Ice and Jungle worlds later in the game.
• Pokemon Red/Blue - I occasionally replay this game with the Pokemon randomizer to spice things up, and every time I get to the Safari Zone my desire to keep playing it dwindles. It isn't an especially hard section, but the limited number of steps you can take discourages experimentation, and you always have to go out of the way to make the same monotonous trek every game in order to get two necessary key items.
• Pokemon Gold/Silver - The Ice Path is obnoxious for similar reasons as the Safari Zone. It's a long arduous trek that ytou have to do every time you replay the game, but doesn't offer much of anything interesting besides ice-based puzzles (yay...) and an admittedly catchy piece of background music.

It's not a game I love but I HATED the find the fucking pixel sections in Metroid: Other M.

I was watching a famous friend of mine stream it on Discord and I couldn't believe that was an actual thing. I mean, I saw reviews of Metroid Other M that criticized those sections before, but I forgot they were a thing. Like jesus .... why? Lol. Especially in a game that's mostly a third person action game! 

Heat Man level in Megaman 2.

Catwoman sections in Arkham City.

The stars in the winged cap stage in Super Mario 64.

The fu#$@ fishing mini game in Twilight Princess.

The "cubic puzzle" stage in God of War 3.

What was bad about Heat Man's stage?