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)
Character mistake: Dissecting the chrysalis, Dr. Roden says that "Somebody grew this guy. Fed him honey and nightshade." Nightshade is indeed one of the typical plants eaten by the Death's head moth, but since "he" is only a pupa, would have not eaten honey, which is something only the adult specimen eats. (00:48:50)
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.
Factual error: Jack Crawford lists Clarice Starling's accomplishments saying that she has a double major in Psych (ology) and Criminology and graduated "magna." Clarice talking with the creepy Dr. Chilton establishes further that she graduated from UVA, where she also followed Crawford's seminar. Problem is, the University of Virginia did not offer a Criminology major in the 90s (does now, but began only in the 00s) and to this day it does not have Latin honors. (00:06:30)