The cutscene at the top of the second level glitched. I get up there and it makes me automatically run off the edge of the screen. I thought it was making me beat the level, and I was mad that it wouldn't let me go back and get the secret. But then the two thugs started getting chopped up by something invisible. I guess that was supposed to be me.
The most annoying thing with the controls is the uncancelable ledge animations. Sometimes I just walk up to a ledge and I don't want to climb on top of it, but then I have to wait for this whole climbing animation.
Also, since your sword activates door controls, sometimes you get locked into the unlock animation in the middle of a fight.