Continuity mistake: In Italy, when Hannibal grabs the glass with a napkin around, the way the napkin is folded changes between shots.
Continuity mistake: In the pig pen, when Clarice is shot down, her gun changes positions between shots.
Visible crew/equipment: When we see the FBI agent running through the woods, if you look at the ground you can see track marks. They are consistently the same distance apart and starts once it goes to the angle from the front. Clearly marks from the tracking camera.
Continuity mistake: In the scene where Hannibal picks up a meat cleaver to chop off the handcuffs attaching him to Starling; in one shot it is covered with chopped herbs, in the next it is clean.
Other mistake: Clarice handcuffed Hannibal. Apparently Hannibal opted to amputate his own hand, but the next scene shows officers descending on Clarice at the lake shore. Had Hannibal amputated his own hand, she would still have been wearing the other cuff. She wasn't.
Suggested correction: It's not known how much time passed between these two scenes. At least enough for Hannibal to tend to his wound and escape. It's quite possible she found the key during that time.
Continuity mistake: In the scene where Clarice wakes up in Krendler's house heavily drugged, she looks at her things on the chest outside of the room. Her denim jacket is there. However, we see her take this off and leave it in her car when she decides to go in to the Verger barn.
Revealing mistake: When Pazzi is killed, there's a shot of his cell phone and phone battery slamming into the ground followed by a splatter of his innards. However, there is a (rather obvious and poorly timed) jump-cut in the middle of the shot, right before his innards splatter down from above. His cell phone is still moving about a bit, when suddenly it goes perfect still in an unnatural way. It also moves ever-so-slightly to the left when the cut happens. It's supposed to appear to be one continuous shot, but it's clear they dropped the cell-phone, waited for it to settle, then dropped the innards and tried to edit it so the shot moved faster.
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.
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.
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.
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.
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 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.)