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The pair got off to a bad start while filming Gone Baby Gone - written and directed by Affleck's brother Ben - when Freeman thought his co-star had turned up late.
Affleck claimed the veteran actor was brought on set too early by mistake and had to wait in his trailer for the rest of the cast to make an appearance.
He told Larry King: "Morgan was fantastic. He is Morgan Freeman. The first day he came to work, everyone is a little on edge because Morgan was coming and it was a big week. And I guess they brought in Morgan a little bit early. You know, they thought he might need a haircut or something.
"But Morgan didn't need a haircut. So he was sitting in his trailer for half an hour, waiting for everyone else to show up. And so when I got there, Morgan had been told that he was waiting there because I was late."
He added that no-one had wanted to admit that they had brought Freeman to the set too early so he got the blame, saying: "So I went up to Morgan's trailer, and knocked on the door. And I thought: 'I'm going to introduce myself to Morgan Freeman.' And he came out and gave me a lecture for 15 minutes about being late and being professional. And so I had to live with that."
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