I am puzzled as to why I'm randomly being shown the animation informing me of the fact that I have just picked up a 5-rupee gem. Those are supposed to play the first time you get one, not randomly throughout the game - right??

Also, there was at least one point in the game where I had to do something to expose something else - I think it was shooting a cannon at a blocked doorway in Snowpeak - where doing it the first time played the apropriate "you revealed something" melody, but doing it a second time later also played the melody even though I'd long since revealed the item/door. (I hope that's clear!)

Another thing. It's not really a bug, but Link's hat doesn't point down when he's upside-down.

After you reload the game, it will play the new rupee discovered thing whenever you find it first time, or if it's in a chest

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Yeah, the whole rupee thing is annoying. That need to fix that so it doesn't do it everytime you start the game. I didn't notice whatever else was pointed out, but something that bothered me was how Link's sword goes throught his hat.