Revealing mistake: When Hannibal slices Pazzi's stomach open, his shirt is open and bloody the whole shot, even before he starts slicing.
Continuity mistake: In the scene where Clarice visits Barney, in each shot the fan switches from off to on and back, both before and after Barney turns it on.
Continuity mistake: When the pigs come out and Hannibal holds Clarice, her left arm is either on her tummy or hanging loose by her side, depending on the shot.
Continuity mistake: When the baddies' car runs Bolton over, he smashes the windshield, but the damage and blood disappear in the next shot.
Continuity mistake: The first time we see Clarice she approaches a car. A bang of hair suddenly appears over her forehead between shots.
Continuity mistake: When the movie begins Barney shows the pink box and places his hand on the string attaching its lid. A frame later, the hand is away but the knot is magically untied.
Visible crew/equipment: When Mason is laying on the hammock, a crew member is reflected on his glasses.
Visible crew/equipment: In the scene after Hannibal escapes agent Clarice in the mall and leaving her shoes as a gift, Mason Verger's henchman that answers his phone in the van has a reflection of a camera crew in his shades. (01:39:05)
Factual error: Clarice shoots the guys in the barn, then handcuffs the fat one, but as she is walking away his arms are spread too far apart to be cuffed. When the pigs come in, we see him dragging his buddy using only one arm with the other at his side, again impossible when cuffed.
Continuity mistake: The letter to Clarice is folded twice when she opens it, yet Hannibal is shown folding it once. (It was not a second fold because we see two edges touch, not a fold and one edge.)
Revealing mistake: When Evelda is killed, her baby is replaced for a blatant, crappy, crummy doll.
Continuity mistake: At the market, when a black thug is crushed between two cars, stones on the white car's roof disappear in the wide angles, but reappear in the close-ups.
Deliberate mistake: In Silence of the Lambs Starling was right-handed. In Hannibal she is left handed because we see her writing with her left. Julianne Moore, the new actress who plays Starling is left handed whereas Jodie Foster was obviously right-handed.
Continuity mistake: The third perfume expert grabs Hannibal's letter with a pair of tweezers on its bottom right corner. In the next shot, he's holding the letter on the top edge. (00:37:35)
Continuity mistake: On the letter, the P.S. read by Hannibal ends with, "So I'm not sure how well I should wish you, but I'm sure we'll have a lot of fun. Ta ta H." But when Krendler looks at the letter on the board, the P.S. ends with, "I'm not sure how well to wish you. Ta ta H." (00:35:40 - 00:44:05)
Continuity mistake: When Inspector Pazzi introduces 'Dr. Fell' to his wife, in a wider shot she has her hand on her husband's shoulder, just sliding off as the shot cuts. In the closer shot we cut to, however, her hand's back on his shoulder. (01:04:53)
Continuity mistake: When Clarice is listening to the tapes from her conversation with Lecter from the first film, Lecter says "You don't have any more vacations to sell to Anthrax Island". But in the original conversation in Silence of the Lambs, Lecter only says "You don't have any more vacations to sell". He never said "...to Anthrax Island". This is arguably a double mistake, as it's part of the conversation that could never have been recorded in the first place anyway. (00:37:10)
Continuity mistake: While Clarice stares at Hannibal's letter, we can hear Hannibal reading it aloud. He says, "Your father, the dead night watchman, figures largely in your value system." Yet on the paper it's, "figures large in your value system." (00:33:45)
Continuity mistake: In the beginning when Clarice and co. are in the van, there is a shot of Clarice sleeping on her back. The next shot shows her sleeping on her side in a foetal position, and then it shifts back to her sleeping on her back when she opens her eyes. (00:04:33)
Answer: In the book it says that Clarice had caught Buffalo Bill before he could. It said also that is why he hated her early in the book.