Deliberate mistake: Skylar's leaving is edited together with footage of Will sitting in a park watching planes take off - including, presumably, her plane. The sun is directly overhead in his scenes, while hers were filmed near sunset. (Most obvious when you see the very long shadows during the same airport footage which is also used in the deleted scene "Pudge Fisk Card"). (01:39:20)

Good Will Hunting (1997)
1 deliberate mistake
Directed by: Gus Van Sant
Starring: Matt Damon, Robin Williams, Ben Affleck, Minnie Driver
Genres: Drama
Continuity mistake: In the construction site scene, you will notice the length of Ben's cigarette fluctuates several times. It actually gets longer/shorter as Ben smokes it.
Trivia: Robin Williams won his only Oscar for his performance as Dr. Sean Maguire in this film.
Question: When Will and his friends leave the Harvard bar, he spots the "Michael Bolton clone" and approaches. He pushes the piece of paper with Skylar's phone number against the glass and shouts "do you like apples?" When the other man replies "Yes", Will says "Well, I got her number. How do you like them apples?" Can anyone please tell me what that means?
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Answer: "How do you like those apples" is an expression used to denote triumph, like "told you so" or "put that in your pipe and smoke it". Will just adds his own little humorous twist to it.
Grumpy Scot