Well, Ocarina of Time itself doesn't really make any sense though that's mainly because time travel is a facepalm of a plot device (Skyward Sword doesn't really make sense for the same reason). The problem is that Nintendo couldn't decide if it wanted a single timeline or multiple timelines then jumps between the two to make the plot work. Then, on top of that Nintendo threw in a parallel universe where Link fails. The alternate/parallel universe/timeline vocabulary makes this even more confusing. Depending on who you talk to, you may get a different definition for each.
Ocarina of Time's story works until it, ironically, starts messing with time travel. After the Forest Temple when Sheik gets the hell out of the way and lets Link use the Pedestal of Time to travel back to the past, the story goes off the deep end. When Link goes back in time and starts changing **** (though why he's a child is a little bit hazy... I'm thinking returning the Master Sword to the pedestal sends Link's consciousness back seven years, maybe?), he technically shouldn't have been able to return to the future he came back from because he should be asleep in the Sacred Realm except now he's not. He's running around finding gauntlets and cutting grass. I believe this is what nickmitch was referring to. The moment Link goes back in time, he should create a new timeline and when he pulls the Master Sword out of the pedestal again, he should go seven years into the future of that new timeline. Of course, that's not what happens in the game. At this point, Link should technically be timeline traveling though it's still treated as a single timeline. He changes the past which inexplicably changes a future he should no longer have access to. If you want to try to simplify this with using a time-loop, be my guest. I think that confuses more than elucidates.
Anyway, everything happens, but that doesn't mean it makes sense that it happens. There is a Ganondorf in the Child Era. After Adult Era Zelda returns Link to the past, we're supposed to assume (that word again) two strings of events occur that creates the official time split (rather than the infinite ones that should occur throughout the game yet don't). First, the Triforce of Courage breaks into eight pieces without Link in that era, he never returns when Ganondorf is revived/escapes the seal, Hyrule is flooded, Ganondorf is revived again and The Wind Waker happens. Second, Link (returned from the Adult Era) finds young Zelda (for the second time total to him, the first in this era to her) and explains everything and somehow they convince the king of Hyrule that Ganondorf is evil. The Sacred Realm is protected (this is in Nintendo's official timeline) and the Door of Time is never opened for Ganondorf to seize the Triforce. Except that doesn't make sense because in Twilight Princess (which follows the Child Era when Link was sent back by Adult Era Zelda) Ganondorf inexplicably has the Triforce of Power that allows him to survive execution and he's sent to the Twilight Realm as a last resort.
To clarify, Ganondorf is sealed in the Sacred Realm in the Adult Era and ultimately banished to the Twilight Realm in the Child Era. So, everything happens (though not all of it works if you ask any questions) and either something is missing between the beginning of the Child Era and Twilight Princess or Nintendo done goofed.
Time travel sounds cool except when you think about it too much. The only anything I felt handled it well is Futurama and I probably would have given it a pass since it's often used for comedic effect.