Continuity mistake: When Silent Bob is telling the Amy story in the diner, his cigarette mysteriously grows from barely above the filter to about half length, then it disappears from his hand entirely, and he draws a new one. (01:30:40)

Chasing Amy (1997)
Ending / spoiler
Directed by: Kevin Smith
Starring: Ben Affleck, Jason Lee, Kevin Smith, Joey Lauren Adams, Jason Mewes, Dwight Ewell
After Holden's disastrous talk with Banky & Alyssa, everyone goes the separate ways. The screen comes up a short time later. It's another ComiCon. We see a banner for a book called "Baby Dave". It's done by Banky, who signing autographs. We also see Alyssa signing copies of her book. Off in the distance, we see Holden. Banky & Holden begin an unspoken dialogue that reminds you how close they once were. After advising him to go "share a moment" with Alyssa, Banky goes back to signing. Holden goes to Alyssa. He puts a book in front of her. Without looking at who's standing there, she passes it back saying it isn't hers. Holden replies that he knows. It's his. Their eyes meet. She looks at the book again. He tells her he finally had something more personal to say. The comic is called Chasing Amy. We see the last page, where Holden (in comics form) says "where ever you are, Alyssa, I'm sorry". She tears up, and tells him she'll read it. He smiles and walks away.
Banky Edwards: Archie is not fucking Mr. Weatherbee!
Trivia: During the lesbian bar scene, they are all around the table. The lights behind them glow eerily like portholes. They re-enact the scene from "Jaws" where they compare injuries, only with cunnilingus stories. Even putting the leg on the table comes from "Jaws." This scene was originally meant to be in Mallrats, but was rejected by the studio.
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Answer: I'm gonna be totally honest... I'm 99% sure there's no significance. In fact, I think it's just stained skin from all the smoking people do in the movie. Most people hold their cigarettes between their first two fingers. And most of the characters are depicted smoking throughout the film, which means they had to smoke a LOT during filming to maintain continuity. I used to get occasional orange (and sometimes yellow or light brown) stains on my fingers and hands when I smoked cigarettes. Especially if I smoked more than one in a short period of time and didn't wash me hands between them. So it's probably just smoking stains on the actor's fingers. In fact, I looked, and you see Banky holding a lit cigarette in his right hand and smoking during the story swapping scene you mentioned, with gives some direct evidence to my theory. (For reference, those stains can wash off with some good scrubbing).
TedStixon