The cover art of the box art for the USA Super Nintendo version shows Marle casting a Fire spell, but she cannot do this as only Lucca as that ability. Marle can only cast Ice spells.
In 600 AD there is a Truce Cathedral where Yakra's hideout is located at and the monsters who hang out there. But in 1000 AD the Truce Cathedral disappears, it's unknown if it got demolished since the game never explains what happened.
When Ayla and her party fight Dalton the boss while on the flying Epoch time machine. Once Dalton is defeated he will get sucked into a time portal and never be seen again. The SNES and PS1 version never explained where he went. This missing plot hole finally shows where Dalton was teleported to at 1000 AD. which is in the bonus dungeon at Dimensional Vortex, if the party defeats him again, he will get angry and threaten to to have Porre invade Guardia which later happens in Chrono Cross. This explains the movie cutscene on PS1, Nintendo DS version, showing the fall of Guardia.
After the party loses the fight against Lavos, they lose Crono who gets killed by Lavos, Schala teleports the party to safety soon afterwards Schala is not seen again. If Magus is kept alive and the party defeats Lavos, he will tell the party that he will look for Schala. The SNES and PS1 version never showed the player if Magus found Schala or not. This missing plot hole finally shows what became of Schala in the DS version. Schala is part of the upgraded version of Lavos called Dream Devourer, if the party is able to beat 3 Dimensional Vortex levels and then defeat the boss, then Magus will reunite with his sister Schala and she will tell him unless people give up their power, Magus cannot hope to save Schala, Magus then gives up his power and loses his memories.
In 600 AD there is a town called Dorino past the Zenan Bridge. But in 1000 AD Dorino has disappeared off the map and is a vast desert likely caused by a skeleton monster Retinite who caused it to be a desert, it's unknown if the monsters led by Magus have invaded the town and destroyed the town or if it got abandoned. Even if Robo restores Fiona Forest and has Fiona Shrine Cathedral, however, the Dorino town still disappears off the face of the earth since the game never explains what happened.