Skirmishes in the old Command & Conquer games... or was it Starcraft? Can't remember which, but for some reason the Computer players always just decided to became allies after a random amount of time. Fucked me over good!

Just recently I was about to give up on Duke Nukem plat during my last trophy (hard play through). The load times everytime you die was unbearable... it wasn't a difficult game just those parts that require multiple tries got so tedius because of the loads. More specifically the octabrain boss. Add in the fact that it wasn't the most enjoyable game I honestly wanted to just get rid of it.

Also, most games that have multiplayer trophies I say fuck that to.

Valkyria Chronicles is one of my favorite games ever but there was this one mission where I wanted to break things. Basically, you had to guard the entrance to the map while still accomplishing your objective on the other side. If an enemy got past you, it was an auto-loss.

In order to prevent that, I would leave two players back in a position where they could cover one another. The problem was, when one enemy would run up, they would TURN TO FOLLOW THAT ENEMY BUT NEVER TURN BACK. ARGH. The guards you had set up perfectly would suddenly be facing the wrong way. That meant that the very next enemy could run right by them without ever being fired upon. Lame, lame, lame.

Also, any FPS that thinks it's clever by adding in platforming sections. Stop it.

Metroid: Other M. It withheld useful abilities from you that you already had, for a very stupid reason.

The last four levels of Zack & Wiki. It tries to turn a puzzle game into an action game, but the controls just don't work for that.

Ugh yes, I gave up on the last level of Zack & Wiki, frigging annoying.
The same can be said for the last level of Trine.

95% of escort missions are simply made to annoy the player. Especially the one where they never wait or follow and run after the first thing they see.

Definitely that San Andreas mission.

I'd also add Spider-Man 2 during the Mysterio mission at the Statue of Liberty. So much frustration from that mission. The game mechanics didn't know what hit them.

The flying missions from San Andreas and Manus from Dark Souls

The San Andreas mission where you're on the beach and you gotta dance to the music and press the buttons

Call of Duty MW 2 makes you kill Russian and American soldiers who have been lied to but believe they are protecting their countries. On those missions I felt like the game was working against me. I don't really care if the game designers though it would be a clever twist in the plot. I'd rather shoot bad guys instead of good guys tricked by bad guys into killing each other. Everyone made such a big deal out of the "No Russian" optional level, but at the end of the game you shoot hundreds of US soldiers to take out the guy who made their deaths meaningless. Great plot device, but I didn't enjoy doing it. Give me evil bad guys over fooled good guys any day.