Radiant Markoth in Hollow Knight is the most correct answer here.

Tyrea in Xenoblade Chronicles 1

Shulk, the main character, cannot damage her with the Monado, but he must be your party, because he’s the only one who can break her monster’s aura. You cannot switch characters in mid-fight, so once the monster is down, you’re stuck with a paperweight ^^;

Hazama in BlazBlue Continuum Shift

This is typical to fighting game bosses, but when that guy can come back from a 75% HP deficit with a long-winded combo and end it with his Astral Heat, there’s just twisting the knife. That’s on Normal difficulty BTW.

Emeraude in Tales of Graces F

This boss has a damaging shield that activates when she moves. This… includes when she takes damage and recoil sback, making any melee character almost useless.

Thunderblight Ganon in Legend of Zelda: Breath of the Wild

The boss moves so fast that it frees itself from your lock-on, and you have a very small window to lock it back on and dodge its attacks when it reappears.

Queen Gibdo in Legend of Zelda: Tears of the Kingdom

The arena has poor visibility, the boss is very fast, your movement can be slowed by the sand and the light rays that you can use to kill the Gibdos… do not affect the Queen, at all. It doesn’t help that Riju’s ability to attack the Queen is slow to activate. Oddly enough, when refighting the Queen in the Underground, I had no problem at all, as there’s no sand and no darkness (provide you light up the root nearby, that is ;) )

Joker from Injustice 2. Not exactly a boss but hated him as a playable as well as an opponent. Also happens to be my most hated fictional character. Found some satisfaction in bashing him with Harley Quinn.