Do you mean Mechior was supposed to be warped instead of just disappear?
The game makes it seem as though he was sent to 1000AD in a gate created by Lavos (Robo said so in my game at least) despite being far from Lavos. However, the Compendium prefers to see it as TB at work.
I think there is a difference between the "real" answer and the answer that makes the most sense. Or, if you would rather, the difference between the developers intentions for what plot points were supposed to be vs what plot points have to mean in order for the story to make sense.
Unfortunately, some of the major plot points have issues with eachother and gameplay that make a unified theory of Chronoverse mechanics pretty much impossible to create. Two examples of such plot points are:
1. Marle vanishes due to variation of Grandfather Paradox - yet this paradox is missing from the rest of the game except for in number 2 below.
2. We see this again on Death Peak: the Crono Team needs an exact clone of Crono to replace the old one, thus "tricking" the past version of the Team into doing exactly what they did last time: try to bring back Crono.
These attempts at preserving continuity are fine on their own - but the rest of the game completely supports TTI, TB, TE, etc, so the Compendium drops the major plot points in favor of gameplay observations. I suppose it would be just as reasonable to do the opposite if you could link the plot points together in a coherent manner.
