Lufia II: Rise of the Sinistrals

I can't answer you as to why the graphics are glitchy at some places ..

But can you tell me where exactly the stairs and chest are that you mean?

C-A

There are no treasure chests when you're still in a submarine, unless you enter a whirlpool.
That's part of the GFX error which is just there (and is a huge inconvenience).

To elaborate on what Khiash has said:
The american version of the game had "tiles" removed due to their religious reference... apparently.
anyways, because those tiles where removed, the game attempts to compensate by applying different image tiles in the shrine. these tiles however are just images, and not interactable, so those chests you "see" are just place holders for other tiles and don't actually exist.