Bug: If you stand in front of a bug or a fish and press start right after swinging a bottle at it, you can put another item in the bottle's place and turn it into another bottle. When this happens, the erased item cannot be recovered, and the new bottle will retain the limitations of the original item (for example, turning the Claim Check into a bottle will still be unable to be used by Young Link.).Piemanmoo
Other mistake: After completing a few tasks at Lon Lon Ranch, Link is rewarded with a dairy cow of his own. But somehow, the cow magically just appears back in his house back at Kokiri Village. His house is basically a tree house way in the air accessible just by a ladder. And the doorway is only big enough really for a small child to enter. Yet somehow a full sized cow is now in the middle of his house. And survives without any grass or water inside.
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Trivia: In the Nintendo 64 version, after getting past all of the guards and making it to the courtyard, look in the right window. You will see pictures of Mario, Peach, Bowser, and Yoshi. Take out the slingshot and hit Mario and you will be rewarded with 20 rupees. In the 3DS version you will see a picture of a level from a Super Mario Bros. game. Look for a question block and hit that with your slingshot to receive the 20 rupees. Do not hit the left window. If you do, a guard will appear and throw a bomb at you.