Factual error: Throughout the film, the supposed rare book experts smoke over and around the books and always handle the books with their bare hands, instead of cotton gloves. Either one of these could destroy the extemely rare books.
Continuity mistake: Near the end, when Frank Langella performs the (flawed) satanic ritual, he pours a ring of gasoline and ignites it, then kneels down to pass his hands through the fire. They digitally inserted the reflection of the fire ring in his eyeglasses for about 10 seconds. Thereafter, his glasses do not reflect the flames, even after he douses himself with gasoline and self-immolates.
Revealing mistake: During the fight scene on the riverbank when the white haired man lands on the pavement, the "concrete" pavement moves.
Continuity mistake: There are four versions of the ninth engraving. Three are intentional, and one is a goof. In the three intentional versions, the female figure resembles the Girl, and is shown with her hand raised, in front of the castle from the film. The unintentional version (the original illustration from the novel, before Polanski decided to make the figures resemble the actors) shows an anonymous female figure with her hand down, touching the beast, in front of an unfamiliar castle which is on fire. The three intentional versions are as follows: 1) The "correct" LCF version found at the end of the movie, showing with the woman with upraised hand, castle matching the one the characters visit, well shaded, and a star/sunburst coming over the wall in the middle. 2) The "forged" LCF version, showing the woman with hand raised and the castle on fire. 3) The AT version, showing the woman's hand up and the correct castle unmarked, with neither flames nor starburst. The goof is visible in the library scene, when Corso compares the Ninth Gate with the reference book. In one shot the ninth engraving is visible in both books and it is the unintentional Version 1: the woman with her hand lowered, and a different style of building in the background. However, in the zoomed shot ~8 seconds later, the castle has changed to the one later seen in the film and on the genuine engraving, and the woman's hand is raised again. In most of the scenes where the ninth engraving is visible, it is the wrong castle/lowered hand version.
Audio problem: After the part where Johnny Depp finds his bookstore friend dead, he gets back in the cab. After driving for a while, he tells the cab driver to pull over to the phone booth. The cab driver says "No problem, sir" but you can see the cab driver's lips in the rear view mirror, and they never move.
Continuity mistake: As Corso leaves Quinta Fargas, he barely dodges a speeding car aiming to ram him. Clasping his canvas bag tightly, never dropping it, he presses his back against a large tree. As the camera cuts to a close-up, the bag is suddenly a yard away from him, on the ground.
Factual error: In Sintra, when Depp and the girl go to Fargas' house in the morning, they ride the motorbike and turn left. However, from Hotel Central to this house you must turn right, it's the road that climbs to the manors, the other way you'll get to Central Village.
Audio problem: While Depp is at 'P y P Ceniza Restauracion De Libros', one of the bookstore owners (man on right side of frame wearing blue apron) says, "I would never have believed she'd parted with it, never." He obviously did not say this. He actually appears to either ask his brother a question or make an entirely different statement.
Factual error: At the end of the movie, the authentic page falls from atop the bookcase. This page appears to be a doubled sized, stapled page - not possible when it was created.
Continuity mistake: At the very end of the movie when Depp is fighting his employer, Depp falls through the floor with his glasses falling to the tip of his his nose. But in the next shot when his employer looks at him, his glasses are all the way up by his eyes. His arms are tied by the floor meaning he couldn't have done it himself.
Factual error: Depp descends from the long-journey train (you can see it's the same train) from Toledo in Sintra. However, no long-journey trains stop in this station, just suburban trains: a direct travel Toledo-Sintra is impossible.
Continuity mistake: Corso has reached Paris, checked into the hotel, and is sitting by a desk in his room to examine the charred remains of the Fargas copy. Look at the tumbler of scotch in this shot. It contains almost an inch of whisky, with ice cubes, and it's standing directly on the wooden desk. Now, as the angle changes and we see Corso from behind, the glass contains very little whisky, no ice cubes, and is standing on a white napkin. It's also more to the right of the book than it was. We can also see several scraps of paper, and what looks to be crumpled tissue, that wasn't there in the previous shot.