On Link's second day in the Market, the sky changes back and forth between full of cloud filled sky with a red tint and a clear blue sky. This continues until Link enters the Temple of Time.
When Link comes down the mountain and returns to Shiek, the conversation changes between a few angles, two of which directly contradict each other. One angle shows buildings and a windmill directly behind them, and the other shows trees.
When Link is playing the ocarina outside the Temple of Time, his finger positions do not line up with what is being played.
When the injured guard walks in on Link and Zelda in the room before they kiss, The guard talks but its clearly not his voice, and his lips are not moving.
In several scenes (particularly during the final battle with Ganondorf) members of crew, like the cameramen, have visible shadows on the ground and are easily spotted if paying attention.