Visible crew/equipment: In the pull-back shot from "Young" Charlie while she's in the library, the shadow of the camera is visible on her back.
Revealing mistake: Towards the end when the Phantom's lair is collapsing, you can see bricks falling into the sewer water and floating. Obviously they were made out of light-weight material and not out of actual stone.
Other mistake: Holmes appears disguised as a Sikh, complete with turban and beard. Although his face is black, his hands are without any make up and are white as snow.