Dwarf Fortress has a very silly difficulty curve consisting of an initial cliff followed by not that much, and all of its options just increase the size of the initial cliff.
Earthbound has some quest chains that can get stuck in really obtuse ways, particularly in Twoson and Fourside.
Crosscode's DLC has that fight where Apollo is way too damn hard all of a sudden.
UFO 50 has ~5 perfunctory games in genres that clearly nobody on the team really cared for, and it's worse for it. That's Fist Hell, Star Waspir, Caramel Caramel, Campanella 3, and Block Koala. There are worse trash fires in the collection, like Hot Foot, but those are at least bad because they tried something interesting and failed.
In Super Metroid, the entrance to Kraid's hideout is poorly telegraphed.
Mario Odyssey giving you moons for every silly little accomplishment is great, but giving the same reward for korok-tier stuff and actual challenges cheapens the reward feeling of actual challenges, and they should've done a tiered system.