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: 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 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: 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)