User blog comment:D. Cello/Assassin's Creed: Revelations (PC) - Official Assassin's Creed Wiki Review/@comment-187.105.170.237-20111221184831/@comment-1153722-20111221203442

Altaïr says he wants to sent the Apple to Cyprus, only it never says he did. In the last Codex page, he still has the Apple with him. He had it with him for his entire life, nothing to contradict that.

In Assassin's Creed it's said that Abstergo had Altaïr's Apple, and it was destroyed in the DIA satellite accident. In Brotherhood, Lucy says that Abstergo wasn't aware of Ezio's Apple of Eden. So they are not a "bunch of retards", it's never stated they are the same Apple. We only assumed as such.