I'll simply use Majora's Mask and Wind Waker.
Ganondorf only got the Triforce of Power because Link opened the door. After Zelda sent Link back in time, Link was to make sure not to open the door. Then Majora's Mask starts.
In the Wind Waker, however, it talks as though Link DID open the door, and that Ganon ruled for seven years until Link decided to wake up and seal Ganon away.
That makes absolutely no sense, as both games come after OoT.