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.
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.).
Other mistake: The guy you give the Rabbit Hood mask to will later challenge you to a race, him on foot and you on your horse. Once he leaves the starting area after the race starts, you never see him again during the race until you get to the bridge. Win or lose, you only see him at the bridge. If you won the race, you should have seen him as you passed him.
Bug: For both the Nintendo 64 version and the Nintendo 3DS version. Go inside the Thieves' Hideout in Gerudo Valley and look for a pot that is boiling. When you do, stand next to it and Navi will appear and turn green indicating that there is something hidden there. However, playing any song on the ocarina will not make anything appear.