The case
Anthony Hopkins' first words to Jodie Foster, through the glass, are "Good morning." Later, on the phone from the Bahamas, it's "Well, Clarice..." The purring "Hello, Clarice" that everyone imitates isn't in the picture.
It's a great impression line, and impressions are how the film lived on in the '90s. The 2001 sequel, Hannibal, finally gave the line a home, which is why it feels canonical.
Why our brains do this
A character's most imitable line is often one the imitators wrote. The impression becomes the memory of the film.
Sources: Wikipedia — The Silence of the Lambs (film) · Wikipedia — False memory: the Mandela effect
