Oh hell, where do I start?
Zero Isles. Just, HOW are you even supposed to get through those things?
World Abyss. I used Wonder Mail to get that dungeon in order to get Giratina after 49 floors of pain. But I get defeated by a ARCEUS DAMNED monster house every time.
Speaking of monster houses, any dungeon with a monster house in.
Sky Stairway. At first, I used Wonder Mail to get that dungeon in order to get a Gengar. Then I found Gengar's were stupidly uncommon and Ghost types attacked me while they were INSIDE A WALL, leaving me to do nothing but slowly die and not be able to do a thing about it.