User blog comment:JAlbor/Wikia at E3 2012/@comment-4681429-20120523203047/@comment-1153722-20120523203530

Altaïr never mentions two Apples... because he didn't have two Apples. It was also a 'failure' how Lucy said in AC1 that Abstergo had Altaïr's Apple but accidentally destroyed it, and then the Apple got shipped to Cyprus in the same holder. It wasn't a failure in Revelations, they cleared up that they are indeed two different Apples. Ezio's Apple was just another Apple that was on Cyprus.