Deliberate mistake: As Christine approaches the Phantom in his lair (just after he has abducted her), we see that she is wearing very dark black eye-shadow. Back in the dressing room after coming off stage, as she talks to Raoul, we saw her face in close up and she was not wearing any eye-shadow at all, even though the Phantom leads her through the mirror just after she has managed to slip on a robe over her undergarments and she has not yet changed to go out to supper (Raoul says she is to be ready in 2 minutes). Her hair becomes 'bigger' and wilder, too. The change in her appearance is a reference to her descending (voluntarily, I might add - he didn't drag her through that mirror) into the Phantom's dark existence and to her sexual awakening.
Continuity mistake: During the Masquerade, there is a close-up of two of the dancers, who sing "But who can name the face?" while standing next to each other, without moving. Next shot, they are several feet apart and the lady is dancing towards where the male dancer is standing.
Continuity mistake: When Raoul is tied to the gate, the ropes across his chest change frequently. Sometimes there are 3 running parallel to each other, from his shoulder to the waist. Other times there is a big knot in the top rope. Still others there appear to be 2 ropes across with a third running straight down his chest between them.
Visible crew/equipment: During the graveyard swordfight, the Phantom's stuntman sometimes visibly replaces Gerard Butler. He has thin and very arched eyebrows and the mask doesn't fit properly around the nose. He is the same stuntman used when Raoul jumps down the hole after the Masquerade.
Continuity mistake: When the Phantom in "Music of the Night" goes to show Christine the wax figure of herself there is a tall lit candle behind him. When she faints he moves in front of it to catch her and when he then moves away the candle is out - the only way the flame could of have been put out was if Christine's hair had smothered it (which would of course have set her hair alight).
Continuity mistake: At the very beginning of the movie when Andre and Firmin first arrive in their coach in front of the opera house, you can see one footman (wearing red) running to meet them from some distance to escort them inside. The camera angle changes and now, that fotman turned into two, standing and even waiting at the coach.
Continuity mistake: On the Opera House's rooftop, the lining of the Phantom's cape goes from light-coloured to black before and after he jumps on the statue. It has nothing to do with lighting, and his waistshirt proves it: much darker than the cape's original lining, it makes it obvious the cape's turned dark since the waistshirt looks paler against it.