The dimensions of Lord Jabbu-Jabbu's insides do not match his size on the outside.
Link uses the Sun Song to hatch the chicken egg. He can also use it to advance time even while carrying a time-sensitive object which is supposed to age.
During the party at Lon Lon Ranch during the end credits, there are several Kokiri around. However, if what one Kokiri says earlier in the game is to be believed, no Kokiri can leave the Kokiri Forest, or they'll vanish. Saria is an exception, since she's a sage, but if what that other Kokiri said is true, the Kokiri that are at the party shouldn't have been able to attend. It's possible the story of Kokiri vanishing if they leave the forest, however, may have just been a false superstition.
Link goes into suspended animation in the Temple of Time as a kid with no earrings. He wakes up with some on, but since he also is wearing a different and larger clothes, leggings, gauntlets, a shirt beneath his tunic, boots, etc., someone (presumably Rauru) must have changed his clothes when his body began outgrowing the old.
The captions spoken by the Sages after getting one of their medallions are all supposed to be spoken from the perspective of the person giving them, but Saria's (Saria will always be your friend) is given in third person for no apparent reason. This is fixed in the 3DS port.
The Fairy Ocarina (which later gets replaced by the Ocarina of Time) is depicted beige with a green triangle on the mouthpiece part in its official artwork and icon of the item in the game, but its in-game model when being used/held is light brown with a green stripe on the mouthpiece.
When Link puts the Master Sword back into the Pedestal of Time, time reverses to seven years prior and the effects are undone, but when he picks up the Master Sword to return to the future, the effects of time and progress are the same from before Link put the Master Sword back into the Pedestal of Time.
Link goes through an underwater warp tunnel linking between Zora's River and the Lost Woods and between Zora's Domain and Lake Hylia without any mention that he would not have been able to breathe underwater while doing this since he does drown if underwater for two minutes as indicated by a timer on the screen unless wearing the Zora Tunic that he can only wear as an adult.
Near the end of Link's main quest as a child before grabbing the Master Sword, he picks up the Ocarina of Time that in turn replaces the Fairy Ocarina he originally received from Saria earlier in the game, without any confirmation of the Fairy Ocarina's fate.
Zelda's alter ego of Sheik has what is physically a male's body but is still female regardless.