I noted a few of them....
No breath in the exterior fortress, no blood on Dorian's sword, No cemetary in Venice (it's be hard to bury someone in a town that is basicly built on stilts), the stuntman in the bar fight, And the fact that the Nautilus proably couldn't get up the Thames submerged and wouldn't fit down the narrow canals of Venice. It's an awesome visual, but could never happen. Espeically since they played the Nautilus up as being so massive.