I'm not sure if this counts but anyway:
1 - Recycling enemies, specially bosses. I can understand recycling enemy guy #37 over and over for an area but when you recycle a boss from one area to another it looks and feels bad. It's specially bad when what used to be a boss is later used as a regular enemy, it makes the previous boss fight and your accomplishment over the boss feel like nothing.
This happens in the Castlevania games, Bayonetta and a few times in the Dark Souls games among others.
2 - Mandatory Boss Rush. I absolutely hate this. It's basically the same as 1 but when a game forces you to beat a boss you've beat before along with several others just so you can continue to the end of the game. It's stupid, lazy and extremely repetitive. I already beat that boss before, why do I need to prove I can do it again? and no, just the fact that you have to do it again and it's a bit harder or you're only on 1 health bar against several in row doesn't make it any better. It's basically the developer saying "we couldn't come up with anything new so here's what you did before a bit harder". Pathetic really. (Optional Boss Rush modes separate from the main story are cool though)
The Mega man games are the worst culprit of this since basically every game in the series does it. I guess it's a tradition by now and if you like it then more power to you but I personally hate it. DMC3 did it as well and it was the worst part of that game.