Since the game is almost a year old, it's been a while since I played it, but didn't Link make his wish before Ghirahim took Zelda to the past? That would mean Link's wish was too soon, Ghirahim was smart enough to wait a while to see what happens, or Link should have thought it through a little more and rephrased his wish in the first place 
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On the other thing, all the games refer to the same Gods, or actually, Goddesses. In Ocarina of Time and in Twilight Princess, they are mentioned as being the creators of the world and the Triforce was left as a side-effect from them leaving the world again. Since a timeframe for how old the world is is never given, they are always the 'old gods', no matter when the game is set. Some games mentioned different gods though (Majora's Mask and Skyward Sword), so it is implied that there exists some kind of hierarchy like in Greek mythology.
And I see others already mentioned the fourth time the full Triforce was used, so that's okay 
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Good questions though!
| F0X said: The Zelda timeline is not even an actual timeline to begin with. It's really a Zelda multiverse in which Nintendo's writers can get away with anything and everything. |
Recently, a timeline was sort of made canon because of it's inclusion in the 'Hyrule Historia' book, which is an official Nintendo release. This basically also confirmes all games occur in the same universe, over a span of many millenia.
You are right that the timeline is not an actual literal telling of history, like in say Star Wars, however. The book mentions a sort of clause. All stories in the games are 'Legends', like the titles say, which means they have been passed down for like thousends of generations and because stories change over time, details can differ between games. For example, to Wind Waker, something like Ocarina of Time happened. To NES Zelda (the original), something like A Link to the Past happened. And so on. The splitting in OoT occurs because of supernatural means, the way the timeline splits from OoT to ALttP is still a matter of debate though as it is not explicitely said in the book. Most have interpreted it as 'Link dies', of which I'm not a fan off, that way you could have a million timelines.
So yes, Nintendo writers can get away with anything .
