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 arms length to the opening above. However, Raoul in the next shot above merely hands down his lantern as if Ledoux is merely a couple of feet away.
When Christine first interprets the role of "Marguerite" in "Faust", we see her 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, we find Christine in the braided wig and outfit worn during "The Jewel Song" which is in Act 3 of the opera.
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.
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.
(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 you are hearing 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. But if you watch, you can see them 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 were clearly 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.