Why can't I find the Wonder Egg in Surrounded Sea?

Question

I am playing Pokemon MD Explorers of Sky post-game and whenever I go to Surrounded Sea, at the end of the dungeon, I see only three Treasure boxes and I cannot find the wonder egg. I have went there many times but no result.

Comments

Are you sure you've never obtained a Manaphy before?

---

Yes. For the first time.

Answer 1

I used an AR code to complete the game but at the saved data it showed to complete the game with the pictures of bosses like Palkia, Manaphy egg, Darkrai, etc. But in the game I have progressed until Surrounded Sea. Because of the hack, I can't progress and it looks like my only option is to start a new game.