For Final Fantasy IV, when Cecil and his allies Rosa, Rydia, Kain, Edge come with him on the Whale spaceship and fly to the moon, they can pilot it until they land it. But when they exit outside, they walk around without their spacesuits. This would cause them to die including Fusoya and Golbez, because first of all, there's no life on the moon including trees or water. Second, they would freeze to death or burn to death by the sun due to extreme heat and cold temperatures caused by the sun or no sun. Also gravity on the moon is different than Earth and they would bounce lightly and float on the moon. If they were provided spacesuits with oxygen tanks, then they would be able to survive on the moons surface but would have limited time to explore and fight before returning on the spaceship. However, their spacesuits would make them more vulnerable to monster attacks and it would be slightly harder to use weapons due to the moons lighter gravity.
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.
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.