Revealing mistake: In the final scene you can see Abruzzi in his cell where they have reused shots from series 1 in Fox River.
Prison Break (2005)
1 mistake in Behind the Eyes - chronological order
Starring: Dominic Purcell, Robert Knepper, Wentworth Miller, Amaury Nolasco
Michael Scofield: I thought your cousin was trying to move in on your girl.
Fernando Sucre: That's my other cousin but thanks for bringing that up, jackass.
Question: How does Don Self know that Miriam should work at Gate when nobody knew about the location of Scylla? Or Whistler wanting to work there?
Answer: Because Miriam was an agent.
But that still doesn't make sense because nobody knew where Scylla was.
He knew that GATE was mentioned in the bird book. He worked with Whistler and had probably discussed GATE with him, so it was clear enough that it was a big part of the plan to get Scylla. Sending an agent to work there in any position would've been a big help for intel, as she could assess the environment and perhaps uncover what Whistler's plan was. He didn't anticipate T-bag's hijacking of the plan, hence why he sent Miriam and not a more combat-trained agent. She was only there for information.
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Answer: Don Self actually worked with Whistler before he died. And Whistler with the bird book actually knew where Scylla was.