I just started playing Twilight Princess yesterday and I've already run into things that I just couldn't figure out even though its my third runthrough of the game!
When I was in twilight before the Forest Temple, I killed two of those bugs that you have to kill to fill up the vessel of light and I couldn't figure out why it wouldn't let me collect them even though I walked right into them. I spent quite a while trying to figure it out but then I realized I didn't even have the vessel of light yet..
When in the forest temple (and I do this every time) I was trying to get the heart piece behind that big flower-like enemy and I was trying to use the spider-bomb that was at the top stairs instead of the ones up at the very top where it's really easy to get at it. I always forget that.
Every time I fight Diababa, I always forget how to kill the main head. Every time I tried to blow the bomb at him, he would shake his head and it wouldn't hurt him. After about 15 minutes, I realized all I had to do was target Ook and Diababa at the same time instead of one at a time.
In ST I also had some stupid moments. This one I just couldn't figure out. In the first or second time in the Tower of Spirits, I didn't know how to cross the lava. I had no clue that I could jump on Zelda's back to cross. My eight-year old brother had to help me with that one..
Another thing in ST: I had no clue how to kill the mothula in the Forest Temple. I was completely stumped and gave up. My 8 year old brother heped me with that one too..
There are probably many more stupid moments but I just can't think of them.