When Meg steps out of the underground river and into the Phantom's lair, her brown pants are clearly soaked with water; a few moments later, when she finds the Phantom's mask in the bedchamber, her pants are perfectly dry.
When Christine lights a candle for her father in the chapel after "Think of Me", she lights her match from another candle. However, when the shot switches to over her shoulder, the candle she lit is the only one burning.
During the Masquerade scene, when the phantom comes downstairs, he has not got the bag with the Don Juan Notes in his hand, but when he arrives at the bottom of the stairs, he throws the bag with the notes on the floor.
At the beginning practice, when the phantom drops the background on Carlotta, he drops a letter down. When it falls down, it is a pure white envelope with the red emblem. When Madam Giry picks it up, the lines on the envelope are outlined in black with the red emblem.
During the "Point of No Return" reprise, the Phantom places the veil on Christine's head. When the camera pans from her face to his, we can clearly see the back of her head, and there is no veil, but when the camera pans back to her it is there again.
When Christine and Raoul kiss on the rooftop, he picks her up and spins around. During this, her hand is on the back of his head, but when the camera goes in for a closer shot, her hand is around his neck.
When Meg goes to look for Christine after she sings 'Think of Me', she walks backstage and passes Monsieur Firmin and Monsieur Andre and stops at the hallway. Then when the camera switches over to the new managers, Meg walks past them again, even though she just went down a hallway.
During the "Point of No Return" scene, the Phantom is clean-shaven. In the following scene in the Phantom's lair, he clearly has a five o'clock shadow, even though the progression of the story is merely minutes.
While Meg is congratulating Christine after her "Think of Me" performance, she puts her hand on Christine's shoulder and then takes if off. When the camera cuts to face Meg, she is taking her hand off Christine's shoulder again.
At the end of "Prima Donna", right before the opera starts, on La Carlotta's left shoulder there are 4 random shapes, but after the Phantom makes his dramatic entrance only 3 shapes are shown - and they are larger than the original 4.
After "All I Ask of You", the Phantom picks up the rose that Christine dropped and slowly tears the petals off in his hand. We see the petals falling as they are torn, but it is easy to see that after the stem of the rose falls, there are less then half of the petals that are on a rose on the ground around the stem.
In the "Point of no Return" scene, when Christine sings "...No dreams within her heart but dreams of love." She has one hand on the basket of flowers. When the camera goes for a wide shot, both hands are holding on to the basket.
During 'Wishing You Were Somehow Here Again', Christine walks up some steps and through an archway. Before she climbs the steps, she is holding a bunch of roses with both hands, clasped in front of her. However, when she walks down the steps, the roses are held at her side, in one hand, under her cloak, before she brings them up and holds them in both hands again
In the final scenes, the position of Raoul's ropes changes between shots. It is easy to notice by comparing his arm's position at the wide angle of the cave (while Christine sings "God give me courage to show you...") to the immediate following shot where she is kissing the Phantom.
During the very final scenes of the movie, when the Phantom is singing "Masquerade" looking at the Monkey, the toy mechanism stops so the cymbals remain in contact. In the following shot, when the Phantom sings "Christine I love you", the cymbals have moved to the opposite position. In the next shot, they are in contact again... and some minute before, when Meg founds the mask, the cymbals have moved again.
On the movie poster, which features the Phantom standing behind Christine, the mask is on the wrong side of his face. It has always been on the other side, and it is on the other side in the movie. Only the poster is incorrect.
When the Phantom takes Christine down to the catacombs for the first time, her hair and makeup slowly change from being simple and understated, to more sophisticated and womanly. The director has stated that this was deliberate and that the change in Christine's appearance during this scene was intended as a metaphor to representing her sexual awakening.
When The Phantom brings Christine to the lair, she is wearing stockings. However once she faints and the scene shifts to the Joseph Buquet scene and then back to the lair, they are mysteriously missing. One explanation for this, however, is that the phantom simply took the liberty of removing Christine's stockings while she was unconscious.
In the beginning, where Raoul is riding his carriage to the Opera House, it looks as if there is a bag of bright blue Ruffles chips in the seat. However, if you look closely it is his family's coat of arms.
When Raoul is on his way down the stairs to the Phantom's lair, he falls through a hole, down into a pit of water. Iron bars then lower from above, but since Raoul fell straight down into the water, it would be impossible for the bars to be there.
When Christine is visiting the cemetery, we see her pass the same set of tombstones (most notably a small stone with an iron fence and a much larger one shaped vaguely like a bed) from three or four different directions before she finally reaches her father's tomb.
The rope that the Phantom cuts and causes the chandelier to crash is hanging limp when it is tied to the rail on the stage, which means that when it was cut it would only probably hang there. If it really was the rope keeping the chandelier suspended then it would be taut because of the weight.
When the Phantom is on the rooftop after Christine and Raoul leave, You see the Phantom's cape blowing in the wind. If you look closely, you can actually see that there are two capes blowing in the wind, one under the other. This is due to the fact that the film editors added a digitally created cape to blow in the background, but for whatever reason, did not match its movements with the real cape the Phantom was wearing.
During Christine's first performance, once the audience appears, if you slow the video down, you can clearly see that the actors in the very back left of the theater are legless mannequins with cloth thrown over the tops.
In the scene of "Don Juan" it shows a birds eye pan over of the audience in the ground level (orchestra seating). The people in the back few rows are not people but figurines of head and torso, they do not have legs.
The last letter that is read in the "Letters" scene does not match the letter that the Phantom is seen to be putting in the envelope. In addition, the text on the letter is obviously too short to match the words that are read by Firmin and spoken by the Phantom.
After the chandelier crash, Raoul and Madame Giry go downstairs to find the Phantom. Despite the scene is composed being three shots taken from different angles, you can easily notice that the stage is always the same, just by paying attention to the cracks and imperfections of handrail bricks.
The lair under the opera is full of chandeliers and torches. Over the years, walls should have been became dirty of soot and smoke (especially the columns where torches are attached). However, all walls are perfectly clean.
The goof items below may give away important plot points.
In the final scenes when Christine sings "This haunted face holds no horror for me now..." she uncovers only one of the two mirrors standing next to each other, but by the time that the Phantom is smashing them, a second is uncovered for his smashing pleasure.
When Meg comes out of the underground tunnel into the Phantom's cave, she has a cross hanging loosely around her neck. But when she finds the Phantom's mask in his bedroom, the necklace is higher on her neck, almost like a choker.
In the first scene of the film at the auction, Old Raoul is referred to as the "Vicomte de Chagny", implying that he has not yet inherited the title of "Comte" from his father (or his older brother as in the book), which would be extremely unlikely given his advanced age. However, even if Raoul was still the Vicomte, Christine would have died as the Vicomtess de Chagny, but her gravestone describes her as the Countess. Either Raoul is the Comte and Christine was the Comtesse (Countess) or Raoul is the Vicomte and Christine was the Vicomtess - you cannot mix and match the titles.