It could be a random glitch. I had a bizarre glitch or two randomly show up when playing Final Fantasy 6 in the past, so it's not inconceivable that there could have been a random error in your CT playthrough somewhere. Admittedly, I don't have the sheer number of playthroughs with Chrono Trigger that I do with other games, so I have never encountered a CT error myself, not even the famed Wolflobe sword!
)
But before jumping to the conclusion that something is majorly wrong with your gamesave, let's rule out some things. While it seems ridiculously simple, have you checked the far, far right end of the platform at the End of Time? If you walk down that little stairway where Magus is standing, the Epoch might be there. (Truth: The first time I played CT I completely missed this somehow, so that's why I bring it up.) At some point Gaspar comments that the Epoch follows the characters around, as if it has a will of its own, so its worth double-checking.
You say you returned to the End of Time via a time gate after defeating outer Lavos. In that case, there isn't going to be a gate that leads back to the Black Omen itself. You can use the bucket gate to get back to the underground cave, which will lead you to the inner Lavos battles. When you returned to the End of Time after the battles, did you use the Time Gates to try and revive Chrono? Or had the Epoch not yet disappeared by that point?
Hmm.... Well, did you perhaps crash the Epoch into Lavos during a trip to 1999 by any chance? I've never followed that course of action, but I think it removes the Epoch from the game (after all, it's wrecked).
I hope something in this jumble of ideas is helpful!