To me, the idea that Link warns Zelda about Ganondorf when after returning to the past is so flawed, I cringe every time I read it. Zelda already had a premonition about Ganondorf, warned her father, and he didn't believe her. So her going to her father again after being told by Link what she already knew, doesn't make a lick of sense. In addition, Link clearly returned to the exact point when he drew the Master Sword  (the Door of Time is open and the three Spiritial Stones are present), which happened AFTER Ganondorf attacked and Impa ran off with Zelda. Not to mention, that there would be two Links present at once if he were sent back earlier. The scene at the end of the credits was simply replaying the moment where Link meets Zelda for the first time, it wasn't showing new events. I understand how easy it is to misinterpret that scene, but the other facts clearly make that the only valid interpretation. So when Link returns the Master Sword to the pedistal (which closes the seal), Ganondorf is already in the Sacred Realm, thus creating the history for A Link to the Past where Ganon has the full Triforce but is unable to return to the Light World.

It only makes sense if link is telling her not to open the sacred realm and to instead hide the ocarina so ganon can't reach it, even then

There are a lot of ways to look at OOT's ending. I typically look at it as that Link tells Zelda of his quest, and they convince the King to come to the Temple of Time. When there, the King learns of Ganondorf's true motives and together with Link his army manages to capture Ganondorf (Perhaps because Ganondorf hasn't quite learned how to control the Power of the Gods yet, I mean, if Ganondorf were powerful enough by himself to take on the full might of Hyrule, then he would have done that instead of pretending to be loyal) and is thus taken to the arbiter's grounds to be executed (And, most likely, the Hyrule army wiped out the Gerudo while they were at it in order to quell any uprising - hence the fact that they do not exist in Twilight Princess.) However, by the time they get him to the Mirror of Twilight for his execution, he is figuring out this new power of his, and thus he is able to use the Triforce of Power against the sages.