There are a couple topics I remember from the game (since I haven't played Chrono Trigger and Chrono Cross in ages) that bug me, concerning the existance of Gates and Magus's assumed ability to continue using them during his search for Schala.
1) As stated in Chrono Trigger, the Gates were most likely created by Lavos and his disruption of the flow of history during his landing in 65,000,000 B.C., creating a time/space rift that allowed Crono and his gang to travel through history. (I believe this is also stated during the Gates explanation at Chronopolis.) However, the Gate Key is the item that Crono and his friends used to actually access the Gates. But as we see in 600 A.D., after the battle with Magus, a giant Gate is formed. I've heard explanations that Lavos caused the Gate to open, after Magus failed to summon him, but why? I believe it was Magus who use his own Dark Magic to open the Gate, hoping to draw Lavos into 600 A.D., fresh from his burrowing into the center of the planet and not yet given time enough to absorb the planet's energies... Perhaps Magus knew Lavos was weak at this point in history, and decided to summon him from that point? But, perhaps Crono broke his concentration (or it might have been on purpose--he may have WANTED to go to 65,000,000 B.C. to face Lavos there--who knows?), all four were drawn into the giant Gate.
2) Leah. "What does Leah have to do with the discussion about Magus?" It's been revealed through an ending in Chrono Cross and most likely by the event planners that Leah is either the mother of Ayla or the daughter of Ayla (I'm sorry, I haven't played the game in ages :| ). How exactly, then, did she arrive in 1010 A.D., in the El Nido Archipelago? Moving back to my first point about Lavos being the reason for the Gates' existance, when Lavos was destroyed, Gates most likely ceased to exist--in T-1, that is. But the Time Devourer--the Angelus Errare to the space beyond time where he existed--lay in Home World. Perhaps the split of worlds really originated in 1000 A.D., when in one world Gates ceased to exist, while in the other, the Time Devourer's influence still allowed them to exist, and the split in time, the split of the Home World and the Another World, happened just as Leah was drifting along the ebb and flow of time, thus bringing her into 1010 A.D.?
I don't quite understand it myself... I do admit, my theory needs a little work. But I do believe Magus would have use Dark Magic to travel through the times after Crono defeated Lavos--if he even time traveled at all. Even if he did, he would be limited to a single dimension, and may have missed the Time Devourer and Schala completely. Who knows. That's just my two cents. :)