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.
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: There are three versions of the ninth engraving. One is the version found at the end of the movie (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). The other versions can both be seen in the library scene. Corso compares the Ninth Gate with the reference book. In one shot the ninth engraving is visible in both books and shows the woman with her hand lowered, and a different style of building in the background. 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: 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.
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.
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.
Other mistake: Toward the end of the movie, as Johnny Depp and his leading lady are being led down into the dungeon, you can actually see the camera bouncing and shaking and hear it hitting the stairs as it moves down the stairs.
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: When Johnny Depp is being shown into Baroness Kessler's room he pulls the strap of his book bag over his head to the other shoulder. Then when he is seen next, it is no longer over his head.
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.