Prior to the release of the Chrono Trigger Prerelease section on the Chrono Compendium, those interested in the Prerelease were either forced to play the game itself, or consult a faulty FAQ by StarNeptune that can be found appended to Meowthnum1's Walkthrough FAQ at Gamefaqs. Its research was mostly truthful, but some information came from a Gamefaqs forums thread, where a few fans falsely posed to be experts on the ROM. These rumors and false assertions can now be debunked, as the Prerelease has been fully explored by the Compendium.
1. Schala and another character were originally party members.
This is untrue for a number of reasons; see Characters (CTP). Gaspar was at one time intended to be the eighth playable character of Chrono Trigger. This plan was likely cut before the Prerelease was issued, as no extra sprites for him appear in the ROM. Toriyama's sketch demonstrates that Gaspar would have worn his Zeal robes and carried his staff in the party. The sketch, and his comment of proof, appear in the Chrono Trigger V-Jump Player's Guide.
2. Schala's hair was originally blonde.
There is really nothing to substantiate this claim, as it is most likely a retroactive assertion made by examining Chrono Cross and Radical Dreamers. Schala's sprite has blue hair in the ROM.
3. A lot of Magus's history was not written into the game.
This is owed to the unfinished state of the game and its dialogue, not any story changes. The person asserting this would have also had to rip dialogue from the Prerelease and translate it from Japanese to verify the absence of Magus's information (the Compendium has since translated the scripts). He fails to mention Magus's history after the Ocean Palace incident, which would constitute most of his personal history.
4. Alfador was supposed to lead you to the Sun Palace, and the quest was supposed to go from there.
The joke that Alfador is the protagonist of Chrono Trigger or the Entity itself is long-running on the Gamefaqs Chrono Trigger forum, and probably yielded this farfetched and absurd idea.
5. The 65000000 B.C. continent is much larger that before.
While the Singing Mountain and Lost Village do appear, the continent is roughly the same size as its Chrono Trigger counterpart.