Dawson Casting: Marilyn Ghigliotti was 33 when she played Veronica, a student in her early 20s.
Enforced Method Acting: An unintentional case. According to the commentary, Jeff Anderson apparently screwed up Randall's "The Reason You Suck" Speech that was directed toward Dante multiple times, so that in the finalized scene when Randall snaps Anderson's rage is 100% real, fueled by how many times he had to do it over.
Executive Meddling: One of the good examples. The original Downer Ending had Dante being murdered by a holdup man but it was never included in any versions of the film. The change was motivated by film guru John Pierson and Brian O'Halloran (who plays Dante), not any execs, though.
Missing Scenes: The scene during the wake, which was later adapted as a comic and an animated short but was never going to be in the movie at all. A better example would be a scene in Big Choice Video, where Randal interacts with a hypercompetent employee named Chet. The footage was burned on the editing machine and mangled beyond use. What little footage survived was used before Caitlin first appears. Some of the audio survived, and can be heard in Snowball Effect, the Clerks making-of documentary on the tenth anniversary DVD set.
Romance on the Set : Jeff Anderson (Randall) and Lisa Spoonauer (Caitlin) dated and later became engaged.
Serendipity Writes The Plot: The Quick-Stop wouldn't let Smith shoot inside during the day, so he had to film all the interior shots at night. To hide this, he came up with the idea of someone putting gum in the locks on the shutters, necessitating them staying closed all day.