There's this one plot hole in Assasins Creed II that really bugs me:
So, after Ezio stops Rodrigo Borgia from getting the Piece of Eden, we fast-foreward a few years in the Animus. Our faithful (if a bit douchy) British friend then suddenly realises that Borgio was a pope. So the expert historian just now realised that the main evil guy and head conspirator was once a POPE? I knew he was a pope from my 10th grade history class!