Temporal Distortions (Cause of)
Four anomalistic instances of temporal distortion occur in Chrono Trigger. Firstly, in the Ocean Palace Incident, strange Gates materialized and gated the Gurus and Janus to various eras across time (and in the new timeline with the Prophet, one would gate Schala to the Darkness Beyond Time). Secondly, Marle's pendant reacted with the Telepod to take her to 600 A.D. Thirdly, Magus's summoning Lavos in 600 A.D. caused a raging temporal distortion that sent Magus to 12000 B.C. and Crono's group to 65000000 B.C. Third, after Crono was at the new Ocean Palace Incident, Schala fell into a dimensional distortion that took her to the Darkness Beyond Time. Last to occur is the new Melchior and Janus's disappearance from 12000 B.C. Who caused these, and why did, in each case, important individuals conveniently go to important eras in the planet's history?
Please note that this entry is better suited for placement in the Common Questions section, but since the answers here are not 100% definitive, the entry is listed under Theory.
Entity Plan and Error
These Gates were all effected by the Entity, whose first action to save itself occurred in 12000 B.C., when it gated Janus and the Gurus to the important eras of its lifetime. The actual Gates in this incident may have been created by Lavos, as he tilts his head toward each person he is gating at the time. Conversely, Lavos doesn't gate Crono and his friends when the incident occurs the second time around, meaning the Entity perhaps created them after all. Secondly, it created the Gates, the one at the Millennial Fair included; once it had found its savior, Crono (as evidenced in the instructional manual, which references "guardian spirits," probably a translation quip, as choosing Crono), the Entity then caused the Gate to open at the Telepod exhibition and start Crono on his quest. Lastly, though Magus's summoning Lavos was the cause of the temporal distortion at his lair, the Entity had a hand in sending the affected individuals to certain eras. If the Entity can create stable wormhole Gates through time, it is not a cop-out to believe that it can usher its own plan along by having an active hand in these instances of time travel. The Entity has much to gain from this course of action. If it is assumed that Lavos would have killed everyone then it would make sense that the Entity would have gated them all to safety. It also follows suit for the places that they were gated to to coincide with any plan that the Entity might have planned before beginning the events that start the game. The group goes back to 65000000 so it can actually see where Lavos originated from.
That said, it is probably not the Entity's doing that Schala was taken to the Darkness Beyond Time through the dimensional distortion in the second Ocean Palace Incident. Whether the planet is aware of Belthasar's Project Kid is debatable, along with whether it even perceived a threat in the form of the Time Devourer, which may have been outside the realm of its perspicacity. Sending Schala to a place where she might evolve with Lavos into a being that could devour time is certainly not in the interests of any reasonable entity, however.
Finally, concerning the disappearance into black Gates of Melchior and Janus in 12000 B.C., this is thought to be an example of the Time Bastard theory in action.