The small, wirring sawblade little orbs in any and all Ratchet and clank games. Where you fight an epic battle, struggling to stay alive by the seat of your pants to finally see the dropship go down with 1 hit point left, only to be hit by one of these guys that was stuck behind scenery somewhere. that was the first controller i ever threw.
The Medusa's in God of War. They'd stop you in your 3 figure hit combo, effectively halting all momentum because you'd have to stop and focus on them exclusively. I've had friends tell me they thought they were easy, and they are if you face them alone, but seeing one pop out of the ground amidst a large mob just makes me sigh.
The Harpies and Shanks in destiny and the flying drones in Wolfenstein : the new order. Both in the same category for being flying enemies in a game that mostly feature enemies on foot. They just destroy my expectations, when i'm behind cover, i expect enemies to come out there and there. And they fly over your cover to mess with that. I know they are designed for that exact reason, but it's just so frustrating to get killed in a corner when i'm catching my breath waiting for my shields to come back up.
Any enemy, that when they have sufficient numbers, are able to stunlock you. I'd have this most frequently in WoW, when i was running a vanilla dungeon for transmog gear and achievements. I know they are meant to be taken on in small groups but for time reasons, you'd pull and entire dungeon, and then get slowly killed by hits doing 1 or 2 damage while you stand there being useless.
The beggars in AC. While not really enemies, they'd throw you down whilst typically running away from guards, allowing them to run up to you and force you, yet again, into combat.
Random, super high-level, encounters in FF9. More specifically, you'd come out of the ice cave at an appropriate level, and you'd run into these overpowered dragons with super high hp pools for that time in-game.
The spiked head goombas in paper mario. Whilst i have to give props to this game for making you strategize your resources whilst still maintaining action in combat due to the action commands. Those spiky heads, especially when in the back rows, just mean you won't be getting out of this battle unscathed, because you'd have to pick out enemies individualy untill you can ge tto them.
The electrified yellow goop enemies in Zelda : Phantom Hourglass. I always think i have time to get a hit in before they electrify.
I seem to have been frustrated by quite a lot of games haven't I? I should mention i have enjoyed every single one of those games immensely, but those few moments just give me the willies.