Continuity mistake: During the fight at the End of the Line Bar, Gem walks and stand next to Castor. Later she move to the left and sits on a couch for the rest of the fight. However, at the very beginning, right after Quorra jumps and protect Sam, there's a brief cut where we can already see her sitting there, too early.

TRON: Legacy (2010)
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Directed by: Joseph Kosinski
Starring: Jeff Bridges, Olivia Wilde, Bruce Boxleitner, Garrett Hedlund
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Kevin Flynn: Your old man's about to knock on the sky and listen to the sound.
Trivia: In the first film, the street sign outside Flynn's Arcade indicates it's on Watseka St. In the second film, the street sign in front indicates the arcade is on Mead St. Also, the surrounding neighborhood seems to have undergone some redevelopment. This isn't really a mistake since a lot can happen in 28 years.
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Chosen answer: He doesn't know Clu is dead. And a little prudence never hurts. Flynn knows Clu and clearly it was entirely possible that Clu was still alive. If they all got back to the portal, it made no difference. If Clu showed up to stop them, Flynn knew what he had to do and needed to make sure that Sam had his disc to get out.
Garlonuss