When you get Vincent in your party, he says "So Sephiroth knows he was created five years ago, and about the Jenova Project?"
But Sephiroth wasn't created five years ago! Sephiroth clones were constructed five years ago (but not from scratch). What is Vincent talking about? Jenova in the form of the Sephiroth-clone?
edit: Also, if you talk to Vincent in Disc I, Cloud says he is formerly of SOLDIER. Does he say that in Disc II or III, when the player knows he isn't from SOLDIER?