the apple Ezio used was supposed to have fallen into the hands of Napoleon and Houdini after Ezio (as stated in the 'Truth' files in AC2). But in Brotherhood, Ezio hid it under the Colosseum, and wasn't discovered again until 2012. Either Houdini put it back under the colosseum (unlikely), Subject 16 got his facts wrong, or there's a huge continuity error.