When the letter is being read by Starling and there is a voiceover by Lecter, we see Lecter playing Johann Sebastian Bach's Goldberg Variations on piano. The keys struck by Lecter and the notes we hear do not match exactly, suggesting Anthony Hopkins mimicked playing the piano for the camera.
On the surround audio track, as heard in cinemas, the drug bust features sounds of gunfire that don't correspond with where the shooters are standing. Also, at least once the camera angle changes and the sound effects remain in the same place.
Hannibal mis-pronounces the word 'tableaux' (plural of 'tableau') as having an 'S' on the end ('tableaus') - an unusual mistake for such a cultured and educated man to make. (However, this may not actually be a mistake on his part, but rather an intended error. There have been times when Dr Lecter purposely mis-pronounces words for the sake of effect, such as the "census taker" speech in The Silence of the Lambs. In that scene (after brow-beating Clarice for her humble West Virginia roots) he pronounces "Chianti" as "Key-ant-y" as a subtle taunting with regards to what he perceives as her uncultured origins.)
In his lecture on Dante's Inferno in the Capponi Library in Florence, Lecter incorrectly assigns the sin of avarice to Pier della Vigna, who died by hanging; Dante emphasizes Vigna's innocence and says he was unjustly accused by envious subordinates, which drove him to suicide. Lecter also inaccurately attributes the quote "I made my own home my gallows" to Vigna, the quote comes from an anonymous Florentine suicide invented by Dante.
When Hannibal is reading newspaper headlines propped up on his piano, one of them purports to be from Washington, D.C. However, the headline uses the British phrasing, "Drugs Bust," instead of the American "Drug Bust," giving away the true source of the printed prop.
In the opening scene, Verger asks Barney questions about Starling's relationship with Lecter that imply it's their first discussion on the subject, yet Verger subsequently tells Barney to "keep all those items from your personal treasure trove coming," implying that they meet on a regular basis.
When Lecter picks up the piece of glass from the broken mirror to give to Verger, he does so with a handkerchief, presumably to avoid leaving fingerprints, but when he hands it to Verger, he does so with a bare hand.
As the Fish Market scene ends with the final car crash, the gang member hanging out of the passenger side of the car is tossed around letting go of the machine gun and partially landing on the hood of the other car, with no gun in hand. In the next shot he has the gun back in his hand.
When Clarice is meeting with the perfume experts, the note from Hannibal is passed to the last person. As he receives the note with the tweezers, he takes it holding it on the bottom corner, in the next scene as he smells it, he is holding it on the top corner.
When Hannibal Lecter undersigns the letter to Clarice Starling, he draws a line above his name from the "b" of Hannibal to the M.D. But when Starling reads the letter the line suddenly starts above the first "n" of Hannibal.
Verger's "good" eye switches sides of his face at various points (likely due to the use of a reversed image); for example, when Clarice first meets him, his left eye is the good eye, but in his last scene in the barn, his good eye is now the right one.
There are several instances while Starling is listening to the recorded conversations from The Silence of the Lambs where the recordings differ from what was said in the movie. In addition some of the recorded conversations never occurred. Also the conversations were supposedly recorded by the doctor in charge of the institution but the conversation that occurred outside the institution while Hannibal was in the cage is still on tape even though the doctor could not have possibly recorded it since he didn't know it was going to happen and stopped it as soon as he found out.
When Mason Verger's Italian pig breeders have the swine devour a mannequin, in one shot a pig deforms the mannequin's face with its giant fangs; in the next shot, the mannequin's head is intact and reinflated with no evidence of the prior abuse that should have left it permanently concave.
In the Fish Market scene near the end when Evelda and Clarice have the shoot out, Evelda's blue scarf is in a different position from when she is shooting the gun, to the next scene when she is shot by Clarice.
When Lecter fights with Pazzi they are standing between the projector and the screen, but you can still see the whole slide. It looks as if the projector has been moved out of the way and the shadow we see is cast by another light source.
The right side of the van following Clarice from her house is damaged with a headlight that does not match the undamaged, left side. Later, as the van is seen before crashing into items, the damage is missing and the headlight matches the other side.
SPOILER:When Mason Verger falls into the pit, the pigs do not come to him immediately. In an attempt to draw their attention, the trainers use a clearly visible broom handle, tapping it against the floor in the lower right hand corner of the screen.
When Pazzi visits the FBI webpage, He clicks on Top Ten Most Wanted Fugitives, which brings him to a restricted access page, where he is required to login. The FBI Top Ten list is viewable by anybody, no need to login.
It is indicated that Hannibal has been removed from the FBI's Ten Most Wanted Fugitives list, only to be put back on it when the investigation is re-activated. However, individuals are only removed from the list if they die, are captured, or charges against them are dropped, so Hannibal should have remained on the list the entire time.
Clarice tells Pazzi that Dr. Lecter killed 3 policemen while in custody in Memphis. Dr. Lecter only killed 2 policemen: Boyle and Pembry. The other people he killed during his escape were the ambulance crew and a tourist, but no third police officer.
As Clarice and Barney are in his apartment discussing the fact that he is dealing in Hannibal Lecter related memorabilia, he bribes her into silence by giving her a block of audio tape cassettes originally recorded by Dr Chilton while Dr Lecter was an inmate at his asylum. However, in The Silence of the Lambs, we see Dr Chilton eavesdropping and recording an actual conversation between agent Starling and Hannibal, yet we see him holding what appears to be a miniature reel-to-reel audio recording unit, which does not use the type of cassettes we see Barney in possession of. Strictly speaking, a reel-to-reel and cassettes are similar in format and mechanics, but there is a large visual difference between the tapes that we see Barney giving Clarice in Hannibal and the tape that we saw actually recording the conversation.
When Lecter writes his first letter to Clarice, he licks the envelope to seal it. When we see it on her desk before she opens it, the only thing keeping it shut is the seal wax in the center. however, Lecter licks the envelope to provide DNA to verify it is not a fake, as he is "re-emerging" from hiding.
When Pazzi is searching for Lecter on the FBI's ten-most-wanted page, the reward is listed as $250,000. Later, the reward is shown as $3,000,000. However, this is a different site. The lower amount is the FBI's reward, while the 3 million is Mason Verger's reward.
When Krendler picks up the faked postcard from Lecter, we can see the handwritten text. The last line reads "Sounds like him to me." This last is clearly a part of the dialogue and was not intended for the text of the postcard.
When Pazzi approaches the library to visit Hannibal and retrieve the suitcases, a group of monks are seen waiting for the camera to reach them in order to start walking down the stairs. Then as soon as Pazzi rings the doorbell, you can see the monks coming back up the stairs behind him.
Immediately after Lecter begins to subdue Pazzi, their shadows are shown against the screen upon which Lecter was displaying his slides for his presentation. Since the projector at the back of the room was the source of the image on the screen, their shadows should have hidden the underlying portions of the image but those portions are clearly still visible, probably from a rear-screen projector.
When Starling puts the handcuffs on Hannibal's hand, you only hear one of the cuffs clicking sound, and there is no sound for the cuffs on her hand. Seconds before it showed her hand with no cuffs, so the cuffs had to be put on around the same time.
In the kitchen scene near the end of the movie when Hannibal has Clarice up against the fridge, she slips the handcuff on him. He then raises his arm showing the handcuff with the key hole clearly visible, in the next shot from a different angle, the key hole is not visible.