That sealed chest is opened by the partially hidden switch. There is no key crystal in that chest though. It's a chunk of laser. Upon examining that map again, it looks as if it doesn't have a key crystal in it. It might not be the only dungeon that's missing one. Rest assured that all you need are 4 key crystals to unlock the Tomb of Apocrypha... though really only 3 if you search the opening area of the Tomb of Apocrypha closely enough.

I apologize for any frustration. I'm not sure why that switch isn't working for you. Chests that are sealed in that way are typically opened mechanically. Barring that, you can blow them up with a megabomb. One megabomb will convert it into a damaged chest, which can then be blown up with another megabomb to open it. It's not ideal, but it might help.

Also heads up that I deliberately placed some decoy switches in another dungeon. They don't do anything except distract from the real solution to the puzzle. Tomb of Seeming. Shovels will help.

Thanks for the reply, I’ll attribute it to a random bug. I’ve finished off everything else you’ve set up and have been quite impressed overall. ^^

Thank you! I appreciate the feedback.