The game follows a storyline and events happen according to that. However, there are a few mistakes that can be spotted that either are not coherent with the rest of the story or have no logical explanation for the time being. As of now, the ones found are:
- Becca, one of Panselo villagers, asks Gale about the location of her little sister Mia. However, there is no NPC in the game called that way. The closest one is Mika, who is working in the fields to the east and fits Becca's dialogue.
- After rescuing Leo, he alongside Thomas, Max and Gale flee to Panselo and reach it by night. Nothing is told about the trip they had to take, but to go from Daea to Panselo they must have travelled through the Misty Gorge and through the broken Atai Bridge, which in the course of the game is not repaired. Both are dangerous places to traverse, as such it probably should have taken them more than a day to get back to Panselo.
- The additional chapter of travelling through the Forgotten Forest involves delivering 30 moonstones to Fran. However, such quantity cannot be found until the player obtains the Rocket Boots, which are found inside Mul Cavern in the Forbidden Lands. Though the game allows the player to go back from there, it might be historically inaccurate to do so in a narrative way.
- The robot found in an abandoned village in the Forgotten Forest is exactly identical to the one in Thomas' Lab, except for the fact that this one drops bombs when dashing to the player. An explanation can be that Thomas did not design the robot in his lab, but found its remains and repaired/modified it.
- When reaching the Stellanite golems in the Ancient's Crater, after they give you the Artifact, one of them compliments Gale for beating the Kobold General, as he saw her through Billy's monitor. However, Gale leaves Billy's golem head at the doorstep of jail B alongside Thomas before heading to the Prince Tower, where the Kobold General is.
- The potion to cure baldness that an elder talks about in Atai is not sold at the potioner's stand.