This happens to me sometimes, and I can't stand it. Usually, what will happen is I'll get stuck in an area, and think of the solution, but do not even attempt it, because I assume what I need to do just isn't possible within the game.
Case in point, Ico. There was only one puzzle I was ever stuck in the game. It was when Yorda is stuck in a sewer walking around in urine and feces, while I'm above her. The solution of the puzzle was to simply lean into a hole and pull her out, the only reason I was stuck was because I didn't think Ico could reach that far or Yorda could jump that high. Turns out I was wrong.
The latest time this happened to me was in Wind Waker, there's a point in some dungeon that you have to use the grappling hook to go over a lava pit, but the place I had to jump to was at a weird angle, and I kept falling into the lava, because I didn't know you could stop, and change your direction. :/
