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, all the known consistencies are as follows:
- Becca, one of the Panselo villagers, asks Gale about the whereabouts of her little sister Mia. However, there is no character called Mia anywhere in the game. The closest one is Mika, who is working in the fields to the east, but she doesn't seem to be related to Becca.
- After rescuing Leo, he along with 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 sidequest 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. Though the game allows the player to go back from there, it might be historically inaccurate to do so in a narrative way.
- The Forest Robot is exactly identical to the one in Thomas's Lab, except for the fact that this one drops bombs when charging at the player. It's unknown how this came to be, but a possible explanation is that the robot in Thomas's Lab is an older model of the Forest Robot that Thomas found and modified to protect his lab.
- After Gale finds Billy's Stellanite soldiers in the Ancient Crater and acquires the Artifact from them, one of them compliments Gale for beating the Kobold General, saying he saw her through Billy's monitor. However, Gale left Billy's golem head in Daea's dungeon before she went to Prince Tower, so it's unknown how he could've witnessed the battle through Billy's monitor.
- The potion to cure baldness that an elder talks about in Atai is not sold at the potioner's stand.