In Fiona's sidequest we are told to visit the sunken desert, the entrance to which is indicated by shifting sands. On the left you can see the image as it appears in-game, and on the right you can see that the screen has a static picture of the sand with swirling effects layered over the top of it. The same is true for the shifting sands inside of the sunken desert.

   

Returning to Guardia Castle we can see a few more things that are not as they should be. The image on the left shows two unused red sprites hidden under the carpet in the entrance hall and the image on the right shows a mass of floor in one of the rooms in the west tower. These images are always here and it would have been possible to include them in Part 1 of this guide, but I feel it would be better to include them here, since at this point in the game we're done with Guardia Castle and no pesky plot points will interrupt our exploring.

Once again in Guardia Castle, we can return to the infirmary and see a wounded man resting in bed. Removing the top layer of sprites shows that the spriters simply cut a sprite in half, rather than taking a full sprite and hiding him. The same thing happens any time a character is lying in bed, but this case is the easiest to see.

Outside Geno Dome we can find this single green square. To do this, I removed the sprite layer that displays craters on the world map (in the screenshot I've also removed the dust layer, but that's just to make things easier to see). Usually the craters simply disappear from the map when their sprite layer is turned off. In fact, in the untouched version of this picture there are four craters including the mystery green one. But in this case, and this case alone, the crater turns into a green square when its sprite layer is turned off. I looked over the whole world map at this point and couldn't find another one, which seems to indicate that this one is something special.

Next, we once again return to Guardia Castle, this time to find the Rainbow Shell. In one of the corridors in the basement we can see this peculiar sight: the wall area is filled with stair sprites. The Gnasher in the wall is not a hidden element as such, since it runs across the corridor you when you enter the room.

   

In the Black Omen we can come across this room. Looking under the floor shows that it hides another, different, pattern on the floor. The hidden floor is on the left, the original is on the right.