Pseudo-Nihilistic Villains
I can't even begin to count the number of games that, instead of making a somewhat nuanced villain with reasonable motivations, make the villain simply want to destroy the world because "Mwahahaha!". Alternatively, they have some lame ass excuse along the lines of "Well suffering is bad and if you're dead you aren't suffering therefore killing everyone is good", which is still pretty damn stupid. This seems to come up more in Japanese games than Western games, and in JRPGs more than other genres, though some series' have a lot of this (I'm looking at you, Final Fantasy!)
Stupidly Huge Healthbars
Some game designers realize that their game needs to ramp up the difficulty. Now, they could do this by increasing enemy variety, changing loadouts, giving the enemies better defensive positions, putting the player in a trickier situation, etc. Instead, what many instead opt to do is simply reuse the same enemies but make their healthbars bigger. This doesn't actually make the game harder, it just makes it long and boring as you spend half a minute completely destroying one guy, knowing that you'll have to repeat this over and over without any real satisfaction.
Ornamental AI Allies
If I have allies with me in a fight, I damn well want them to do something! It's really stupid if you have a small army on your side, but they can't hit anything/don't help in the slightest, meaning I still have to kill all of the enemies on my own. On the other hand, this can be inverted to negative effect:
Overpowered AI Allies
Sometimes, the game opts to make your friendlies so damn powerful that they can win the battle while you cower behind a wall waiting for it to all be over. I don't necessarily disapprove of this in certain situations (see: once you reach the "tipping point" in Space Rangers), but winning a game should involve more effort than taking cover and waiting for it to all be over. Special mention goes to Haze, where you initially have drugged up guys in super armour on your side that are basically invincible, but when you switch sides you discover that the khaki wearing guerrillas have somehow made their skin bulletproof and invented armour piercing rounds.