It's time being all wibbly-wobbly.
Suppose this is the original timeline, where the three Gurus + Janus were sent into the future.
-------->------------------>---------------------->------------>-O (Gaspar)
| | | |
| | (Janus) | (Melchior) | (Belthasar)
| V V V
----O---------O---------O------------------O---------O-----------O------->
(65m BC) (12m BC) (600 AD) (1000 AD) (1999 AD) (2300 AD)
Once you start time traveling with Crono & co., we gotta start looking at each person's
respective perspective.
----O---------O---------O------------------O---------O-----------O------->
(65m BC) (12m BC) (600 AD) (1000 AD) (1999 AD) (2300 AD)
^ ^ |
| | |
| | (Crono) V
<---------<-------------------
We play as Crono
after Melchior has arrived in 1000 AD. When we travel to 12m BC, we arrive
before Melchior was ever sent to the future. Thus, we are able to see him both in the present and at Mt. Woe; it's the same Melchior, just at different points in his life.
The same is true for Janus. We meet him in 600 AD as the older Magus, way after he first arrived from 12m BC. The Janus we meet in Zeal
is Magus, only young and before he was flung to the future to
become Magus. Only now we have two Magus's (young Janus and the Prophet) in the same place because
our older Magus traveled back in time as well.
Chrono Trigger almost never* demonstrates a grandfather paradox, so this is allowed.
Since we first control Crono in 1000 AD, the awakening of Lavos that sent the Gurus and Janus to their futures did and always will happen. Otherwise, we wouldn't have a Crono to play as. And since grandfather paradoxes don't exist in
Trigger, we're allowed to have multiples of any character at any given moment(s).
As for Toma... Yeah, he literally has a family tree of men named Toma, haha. I think the one in 1000 AD is the 13th? He never time travels.