Continuity mistake: When Lecter is in the ambulance, wearing another man's face, as the ambulance officer has his back to Lecter, Lecter takes the large dressing off his face and pulls the oxygen mask down, then sits up, but when he does, the oxygen mask would be in the way; it is around his neck, he would have had to pull it over his head to get rid of it, but he didn't do this - the oxygen mask vanishes. (01:25:05)
Factual error: In the scene where the police are preparing to raid the house in Calumet City, IL, you can see hills in the background. Calumet City is about 25 miles south of Chicago - there are no hills like that for hundreds of miles in any direction. (01:37:30)
Continuity mistake: Before Clarice chases Buffalo Bill down the basement steps, she quickly slips off her green overcoat, letting it fall to the floor. (I wasn't able to see if the green/red checked blazer and/or the grey scarf she almost always wore were slipped off at the same time - the view was obstructed by a table.) After Bill is killed, Clarice exits the house and comes down the front steps wearing the green/red checked suit jacket (blazer), but does not have the green overcoat or scarf with her. (01:43:13 - 01:50:17)
Continuity mistake: When Clarice is searching the basement, the first door she approaches is hinged on the left and opens towards her. She opens it, and it turns into a door that has the hinges on the right and opens away from her. (01:43:50)
Suggested correction: There are two doors in that part of the basement. The one she enters is hinged on the left and opens inward. But the other door - the one she exited through to look for Jame Gumb - is hinged on the right and swings outward.
Visible crew/equipment: At the end of the film, when Hannibal is telling Clarice about having "an old friend for dinner" a camera crew is reflected in his sunglasses. (01:52:30)
Plot hole: It makes absolutely no sense that there would be over a dozen cops and soldiers in the lobby of the courthouse and leave only two cops to guard Lecter regardless that he was locked in the makeshift cell. Yes the plot needs a reason for him to easily escape but this still goes against every conceivable protocol for such a dangerous prisoner especially when there were dozens of armed personnel just in the scene alone when he was being transferred from the plane.
Factual error: Many of the vehicles in the movie have Pennsylvania inspection stickers on the lower driver's side windshield. This is not surprising being that most of the movie was filmed in Pennsylvania. However, they should have been removed when the car is suppose to be from another state. For example, the Senator's daughter, just before her abduction in Tennessee, is seen driving a car with Pennsylvania inspection stickers. Also, the driver for Yourself Storage in Baltimore also has Pennsylvania stickers on his car.
Continuity mistake: At the beginning when Clarice is jogging through the woods, the sweat on her sweatshirt varies from shot to shot.
Continuity mistake: At the graduation ceremony, a woman cuts a slice of cake and passes it to someone and then, without slicing the cake again, she somehow has another slice to pass to someone else.
Suggested correction: She actually hands the person an empty clear glass dish (the kind used to serve the first piece of cake); the person must have wanted the dish to get something else, not cake.
Other mistake: After Clarice is finished interviewing Frederica Bimmel's friend, they cut to the abandoned house in Calumet City IL. The front yard is full of leaves, but yet there is only 1 lone (pine) tree in the yard, and the homes on either side do not have visible trees either.
Character mistake: Buffalo Bill's revolver is a double action, meaning did not need to cock his gun before firing it (you only need to do so with single-action revolvers. Cocking a double-action just makes the next trigger pull easier.) He could've just shot Starling. His stupidity got him killed.
Continuity mistake: At Chicago, when Crawford and his team are about to break in to the empty house, the red ribbon on the flower box covers both the lid and the box when the agent takes it out of his car. When he rings the bell, the ribbon only covers the lid.
Deliberate mistake: The number of acts Lecter performed during his escape from the individual jail cell and until he was attended to by an officer (who thought he was an injured officer) would have taken a lot of time and effort to complete - way more time than he could have gone undetected by one of the many officers in the building. Slashing/ bludgeoning to death a person can be done fairly quickly (munching on a victim's face adds time!), but three particular acts required a substantial amount of time, especially for an elderly man whose ultimate goal was escape: Swapping clothes (undressing and dressing) with a police officer and trimming off his face/scalp to appear to be that officer, then getting to a strategic location to be discovered; Setting a dead officer on the roof of the elevator; and, somehow hanging / impaling (crucifixion-style) an officer from the top of the jail cell (which appeared to be around 10' high). The latter feat would be challenging for TWO physically-fit officers.
Character mistake: Clarice was given clear, explicit instructions by Crawford before going to the asylum to see Lecter, including: do not touch the glass; do not approach the glass; tell him nothing personal; do not accept anything from him. Barney also gave the specific rules to Clarice when she got there (e.g, "you don't get near the glass"; use the food tray carrier to give him papers), and informed her he would be watching her on video. An FBI Agent TRAINEE is under close scrutiny and failure to meet the high standards and/or rigorous training can/will result in dismissal from the academy; a student must follow the rules and demonstrate she has what it takes to graduate and is suitable to become a member of the FBI. Given the high standards and relative difficulty in securing a position with the FBI, a trainee would not blatantly break the rules or virtually disregard the direct orders of a supervisor like Clarice did - especially during the very first assignment. The end does not justify the means.
Factual error: When Starling leaves from Memphis, the jet shown taking off is in St Louis, not Memphis. This can be noted by not just the McDonnell Douglas sign, but the fact that the sign is on their Headquarters Hangar, which is in St. Louis. I have lived in St louis all my life: there is no mistaking this sign and building (even in the dark) for another hangar or sign in another city. It also helps to know McDonnell Douglas had no hangar in Memphis, nor any buildings with any signage at the time of the movie at all.
Plot hole: When Clarice visits Lecter in his new makeshift cell, she brings his drawings, which were left behind in Baltimore. She tells him how she saw the lambs being killed and heard them screaming, taking one lamb with her when she ran away. As the guards approached his cell after she leaves, the camera pans across the cell, taking in the drawings Clarice had brought, and the top one is a very detailed drawing of Clarice holding a spring lamb. She only told just told Lecter about the lamb, not enough time for him to have done that drawing.
Suggested correction: First; I do agree and support the mistake. But playing devil's advocate for a moment; she told him back in Baltimore about the ranch and how they had sheep and horses, so in theory he could have already started drawing back then and figure that a memory about the place was linked to those animals, adding the exact detail afterwards. Should also be noted that the guards approach the cell 'after she leaves', yes, but it's an 'after' that happens after she already flew back all the way from Memphis, so a few hours later.
Your last sentence corrects the mistake, the top drawing is new and wasn't brought by Clarice. You can see chalk on top of the drawing indicating he had just made it. Several hours passed between her delivering her story and him receiving his dinner.
Continuity mistake: When Lecter is about to kill the two cops guarding him, he kicks the cell door preventing one of the cops from entering the cell. Just a moment later he is in front of the guard and there is no metal door in between them.
Revealing mistake: When Clarice goes to Crawford's office, on the board there is a newspaper article titled "Bill Attacks Again, Woman Missing..." on the left and another titled "FBI Links 'Skinning..." on the right. The three top paragraphs on the left columns of both are identical (with different spacing). Two of the yellow lines on the right one are the same too.
Continuity mistake: When Hannibal is moved to another city, and shots are heard, 5 police officers go up to investigate, but when they burst into the room, now there are 6.
