A few spring the mind.

1) Whitney (Pokemon Gold et al)

This one probably only works if you're 12, but on behalf of basically every 12 year old on the planet back then: little miss rolling cow can fuck right off. It was the near perfect balance of overpowered (Rollout reliably stomping everything that didn't resist it - with nothing more interesting than Geodude capable of resisting it available prior to that point in the game) and really fucking annoying - with attract randomly disabling half your team and incessant recovery spam dragging the battle out six turns longer than it should be.

2) Whatever the fuck I fought at the end of Infamous.

Probably one of the most forgettable video games I ever bothered to complete, to the point that I have literally no idea what the final boss even was - but I do recall it taking fucking forever. Not due to challenge, which certainly wasn't there; just as a result of having one of the most obnoxiously long health bars I've ever seen. Also, is my hazy recollections are correct; Infamous didn't let you auto fire, so you had to be tapping left trigger none stop for the entire fight. If a boss carries an RSI warning then it is not well designed.

3) Caulder (Advance Wars, Days of Ruin)

The final missions of Advance Wars got progressively shittier with each iteration, but DoR was the unambiguous nadir of the series. You're given a huge map with tons of bases and cities to capture and an enormous, powerful enemy to overcome, and literally the only method to win is to ignore all of it. If you rush the mission objective right from the start you can clear the whole map in 7 turns. If you don't, and try to actually play the game, it is functionally impossible to win due to the power of your opponent and the arbitrary time limit imposed upon you. Now this, while disappointing, would not in itself merit a black mark, except the game repeatedly tells you that you need to build up your army and resources in order to win, both in terms of how you've been conditioned by the rest of the game, and what your support characters literally say right before the final battle.

4) Most of Bravely Default past about the sixth iteration.

I love the idea of an RPG where you're expected to be at level 99 with everything maxed out for half the game, and the challenge comes from finding the right combinations of skills and abilities to clear the battles. The problem comes from the fact that, in Bravely Default, past a certain point, the power level of enemies rises to the point that you're just abusing the same strategy for basically every fight, exploiting the Ninja's Utsusemi ability or the Spiritmaster's Stillness. This makes battles incredibly slow and repetitive, and from this point on you are expected to fight the same bosses over and over again, just with higher and higher HP totals.

5) Tower Knight (Demon's Souls)

This fight is fine but for one glaring problem. You are supposed to attack his feet to knock him over (Jason vs Talos style) but to game gives you absolutely no feedback when so doing that your attacks are accomplishing anything. As such I attacked his feet a few times since it seemed like the obvious thing to do, concluded that it wasn't having an effect and spent the best part of an hour trying, unsuccessfully, to work out a different strategy.

6) That fucking table (Persona 3)

It's a table. Sometimes that's enough.