Mass Effect 2: Implausibly uncooperative Council and former teammates, a little too much pandering to guys who want to see women in tight or no clothing. Someone who has no business designing game mechanics responded to complaints of boring planetary exploration by creating an even more boring planetary scanning mechanic. Particularly irritating because they had a much better solution already in place: the containers of materials scattered throughout the various stages. All they had to do was not make the amounts in those containers negligible, and it would have been fine. Not ideal (I actually liked the Mako and the sense of exploring planets), but certainly better than what they did.
Red Dead Redemption: Euphoria engine emphasizes aesthetics of motion over player's control, results in a Marston that sometimes walks or runs like a drunk even while sober, and for a seasoned fighter takes an incredibly long time to get up after a fall. Rockstar's weird fetish for closing off areas of the open world for arbitrary reasons also breaks the immersion once in a while. You can fire directly away from a civilian at a predator or bandit that's already attacked them, and they'll shoot you for it and keep shooting until either they or you are dead, forcing you to commit a crime. Guys who get guns shot out of their hands will bend down and pick them back up while you still have your gun trained on them. No sane human being should ever do this and expect to live.
Assassin's Creed series: WAY too much of a disconnect between what the player inputs and what the character does. You can press x to assassinate the soldier right in front of you, and Ezio will turn and double-assassinate two civilians to the side of him, 90° away from the direction you were pointing him in. If we're trying to follow the Creed, so should Ezio. Running, jumping, and fighting all have similarly epic failures when the AI interpreter makes poor decisions. 100% synchronization often fails because of aforementioned misinterpretations, and also because the system itself is buggy. One mission in Brotherhood requires you to kill several sets of targets using your recruits. If you watch the recruits kill the targets, you pass. If you signal them and turn your back, you fail as soon as the targets are killed, even if you heard two hidden blades, turn around, and see two recruits running away from two corpses. Someone wasn't earning their wages at Ubisoft.
Minecraft: Mojang have contracted Bay12 Syndrome: New features are added, old features are broken, and are left broken as the team goes on to add more new features. Less understandable with Minecraft, as it is (supposedly) a full release and not an alpha like Dwarf Fortress. Examples: It is now nearly impossible to fight spiders or endermen on a level field without being hit, as the server records their hit before your client shows them in melee range. A similar problem with Ghast fireballs makes it actually impossible to reflect them without moving out of the way; the fireball is only reflected a few tenths of a second after you hit it, by which point it has traveled a few meters past the point where it was hit. As a result, if you were standing still while reflecting it, you get hit by it before it registers the reflection. This problem is most annoying with the poisonous cave spiders. As discussed widely on the forums, this happens to a lot of people, whether they're running infected 5 year old laptops or squeaky clean $3,000 brand-new gaming rigs.
Prototype: Maybe not one of my top 5, but I keep coming back to it every year or so, so it's doing something right, and I'm playing it now. Great gameplay, but the thing about "the game will select the most important target" is a dirty lie. Bewilderingly, they have a decently written plot and a good actor for the protagonist and the WOI dialogs are not bad at all, but in cutscenes they still manage to churn out some of the most cringe-inducingly inane or overly angsty lines I've ever heard in a game. The objectives for some timed events are randomly placed, but no consideration is given to travel time or time allotted, so you'll sometimes be given a set of objectives that can be reached in 3 minutes, but you're only given two. Similarly, Web of Intrigue targets are often spawned blocks away from you in areas that are fatal within a matter of seconds. It's very common to see a target blink onscreen and then die less than two seconds later, and they don't respawn until a day or so passes in-game. One escort mission has an escort target with AI that can't reliably navigate routes cluttered with debris, in a city where the streets are filled with ruined cars and large pieces of buildings.