Just an opinion, but after watching the movie again, I noticed that some locations in the movie looked a lot like certain (other) places in AC2.
In the third episode for example, though it's supposedly St. Peter's Basilica in Rome, the church where Borgia hits Giovanni with a throwing knife looks a lot like the inside of the Santa Maria dei Frari (the Venice DLC Templar Lair). Also, in the last scene of Borgia talking to the other Templars, the room looks a lot like Leonardo's workshop (particularly the fireplace and the arched doorway on the left where Leonardo has Ezio hide a guard's body at one point).
They're probably just animation budget cuts or something, but did anyone else catch that? :)