Even if he isn't told about Meilin's dog, Ark still knows the dog is named Turbo.
The save book on the desk in the inn in Litz is not there during the night.
Things such as stoves are still working even when no one is around to use them.
Some houses do not have beds in them.
Evegreen shows up as a lake on the map, but is a fiery area.
Greenery covering the world is only a palette swap; there are trees visible before this.
Even after traveling hundreds of miles on the map, Ark's wounds only heal when he uses medicine and never heal over time.
The planet is said to be of 46 billion years. This is several times the age of the universe.
It would take months or even years to travel the distances in the game.
Lei, somehow arrives on an entirely different continent and it is never explained how this has happened.
No explanation is given as to why there are cannons inside the final dungeon.
Pierre doesn't recognize Ark even after meeting him a couple of times.
The 'time bombs' on the flying fortress are remote-controlled, not timed.