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Manhattan leaked before they even started work.
From memory, a sci-fi magazine seller figured it out, just based on address changes. He even figured out it was likely an attempt to make an atomic bomb. The USSR also had it completely compromised. The first soviet bomb was basically a direct copy of the American one.
That was also with most/all the workers in 1 location. They also had a very good reason to maintain security (grunts on the ground, not just leadership).
Wasn't the Manhattan project compromised from within because of communist sympathizers, or even outright communists working on the project?
Depends what you mean by compromised.
Some of the scientists there were communists, or at least sympathetic to the communist cause. Since the USSR was currently an ally, they leaked information to them.
Other scientists didn't follow security rules, either because they didn't care, they hated the lockdown, or they wanted a challenge. Information slipped out because of that, even if it wasn't a deliberate attempt to compromise the security of the project.
I wish Oppenheimer had spent less time on the trial, and more time on some of the really interesting scientists on the project. People like Richard Feynman, who was famous for playing bongos, trying to learn throat singing, and cracking the safes on campus just for fun. And, although slightly after the war, Louis Slotin and the Demon Core incident would have been an excellent scene for a movie.
This is what I mean by compromised.
Correct, though that wasn't the only leak, just the most serious.