The inside of buildings and the ship do not match the outside.
Grammar mistakes in in-game text.
The Monster Corral lacks a gate. Corrals always have gates.
The customized layout does not match the background map.
At Home, NPCs continue to build shops without ever being invited to do so.
At the tower, Pearl says that Erazul will be mad at her if she doesn't hurry, yet Erazul never passed the party on the way down.
When the Player first gets an elemental coin, an NPC refers to two spirits as one.