Plot hole: The Triforce of Wisdom is kept in Link's room up in a tower. It does seem logical to keep it with Hyrule's greatest hero to keep safe, but that's all you ever see protecting it. Hyrule is a large kingdom, and the Triforce of Wisdom is a vital part of keeping their community safe. Yet the only one protecting it is Link. And he's not with it 24/7. The room is not very secure either and is breached all the time by Ganon's forces. A kingdom like this would have knights to post all around the tower and be in Link's room when he's away. But nope, not here.
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Plot hole: Link goes after Ganon to save the King and winds up hanging on the tail of his Unicorn Pegasus in the air. Zelda was in her room in a high tower when Link used the diving board to get out to an even higher tower. Ganon blasts Link off his horse, and Link begins falling to certain doom towards the castle grounds. But miraculously, Zelda is there with a hay cart and saves him. She was all the way up in her tower and Link wasn't even out of the room for 2 full minutes. Yet somehow she was able to make it all the way down to the castle grounds, grab a hay cart, and be in just the right spot to catch Link.