Some character portraits do not match their character models.
Some characters make contradictory statements, which can only mean translation mistakes.
In the water temple, a big stone is shown to float into place when water is released into the pool wherein it is contained. Stones do not float.
Bows can be seen being stored in the game which are much taller than the average NPC. A bow cannot be taller than a man, for any taller than that is impossible to handle.
The picture for the Left Mask Fragment is a picture of the right side of a mask.
The second-to-last dungeon has items that can only be used in towns, even though there is no opportunity to go to a town between the second-to-last and last dungeons.
The last boss gives experience points despite there being no further need for leveling.
The globe in Eldeel's lab is of Earth, which is not what the world of Ys's canon looks like.
Even having been given the freedom of the town, the team while in Highland Town still must exit the mayor's house by the window at night because the front door is locked.
Karna says that Adol got into trouble because Karna climbed a wall, but Adol didn't get into trouble.