When Christine first interprets the role of "Marguerite" in "Faust", she is in the costume used for the ending of Act 5 of "Faust" (the finale of the opera). However, when Raoul comes around to her dressing room, after the opera has finished, she is in the braided wig and outfit worn during "The Jewel Song" which is in Act 3 of the opera.

Raoul reads Christine's message with the card in his right hand. The closeup, however, shows the card being held in the left hand.

When Raoul and Ledoux are approaching the Phantom's lair, Ledoux makes a drop through a trapdoor about 10 or 12 feet down, clearly out of arm's length to the opening above. However, in the next shot, Raoul merely hands down his lantern as if Ledoux is only a couple of feet away.

There is a lack of continuity of Erik's sleeves during the unmasking.

1929 cut: The flickering of lights just before the chandelier falls are on faders during the reshot footage. During the cross-cutting with the 1925 footage, however, they are on breakers.

The opening credits are accurate to the 1929 re-edited version, listing Mary Fabian as Carlotta and Virginia Pearson as Carlotta's mother; however, the ending credits still credit Pearson as Carlotta. This is due to the fact that the "1929" cut is actually made of two negatives: one from a 1929 silent version and one from the original 1925 version. It's most likely that the credit sequence is from the latter.

(1929 cut) When the Phantom's alarm goes off, the sound of the chimes does not always match the striking of the device's "arms". That is because what is heard is the film's soundtrack, not "sound effects", which do not exist in a silent film. As such, this being "off sync" is allowable.

When the crowd grabs Erik alongside the Seine, they are in such a rage that some people accidentally fall into the river. However, it appears they deliberately run and jump into the water, rather than being pushed or jostled. Another one runs down the stairs and is about to jump just as the scene ends.

Parts of the unmasking scene clearly were filmed on days when Lon Chaney didn't wear his character makeup. When he has the mask on, his ears are not glued back, which suggests that his face was 'au naturel' underneath the mask.

When the front page of the newspaper "Le Matin" is shown, its higher part is written in French, while its bottom part is written in English. Although main titles make sense in both languages, it appears that lines hardly form a consistent text and are closer to gibberish.

During the coach chase, Lon Chaney did not apply the Phantom's skull-face makeup to his nose.

1929 cut: A shadow can be seen passing in front of the backlighting of the door to Christine's room in the Phantom's lair just as the unmasking scene ends.

When entering , Ledoux tells Raoul to keep his hand up as the "strangler's noose coils quick". They are then seen walking with their arms up as if they're in school trying to be called on by the teacher. The "quick" noose coil could easily encircle only their head due to the wide space between head and upraised hand. It was make more sense to put one's hand directly on the head - then the noose would not be able to slip around only the head.