I can think of many...
How about the overuse of unnecessary puzzles in Resident Evil 4? If I wanted to play a puzzle game, then I would play Professor Layton, not a zombie game. That was the only real setback in my opinion. I mean, if you don't count the atrocious voice acting which means nothing to me then the stupid puzzles set it back.
The many fetch quests in BioShock. I also love BioShock but the fetch quests were so annoying... I mean, you finally fought your way through a field of splicers and Big Daddies when you get a message telling you to go back, pick up a missile thing, and bring it all the way back. That is artificial game lengthening and it is not cool.
This dam level in Call of Duty 1. Now Call of Duty has a very special place in my heart as the first shooter I've ever played and it is a fantastic game but every time I think of one flaw in the game I always think of the dam level. See, the idea was you were supposed to fight you way through this dam and then set explosives at the bottom and then come back up. But the thing about the dam was that every wall was white and every room was identical to the next... and it was enormous. So it was nearly like a maze and some invisible enemies hiding in places you can't reach. So I ended up walking around in circles for nearly thirty minutes without seeing anyone.
The tank on the ice level of Gears of War 2. There was a section of Gears of War 2 I'm pretty sure everyone remembers where you have to drive a tank over snow and ice to get into this cave. Then you go over an ice pond and something is falling into the ice and making holes. Normally these holes appear right in front of you and you almost immediately fall in due to crappy tank controls. Then after you navigate past the ice, there is a sort of mini base set up long range. Shooting at a base long range with a tank is not making a challenge, that's just not cool. Especially on insane where your tank blows up after four hits, you can't get close enough or you'll be in their range. I wish that they just removed vehicle sections from games.
And now I have to criticize my beloved Professor Layton series... The one thing that I found slightly weird was the way that the people gave puzzles. I mean, most of the time you'll be just talking to someone and they'll have an awkward transition into a puzzle. I don't really know how else they would have done it, but it seems like everyone memorized a puzzle and is trying to force it on to you. It's hard to explain... you know how when someone learns a new word and they try to use it as much as possible, even when it would make more sense to use another word? It's kind of like that except instead of a word, it's a puzzle and you just happen to be the only person that talks to them.