There was an interesting story that ran this morning on NPR (transcript here)
about the fact that despite all of the secrecy surrounding the Manhattan Project, the U.S. Government was secretly patenting the various components of the first atomic bombs and related nuclear technology. This was done apparently to ensure that the U.S. Government would have monopoly control over nuclear technology after the war (as opposed to those pesky scientist actually creating the technology), despite the fact that the process of filing for a patent could itself pose a security risk. To quote the article
Even during the war, some people feared the patent project might backfire. They worried that spies might be able to figure out that the United States was developing a bomb by trying to submit their own patent applications. Outsiders who filed patent applications on related topics got a note back saying their patent had been stamped secret, a clue that the government deemed the topic sensitive.
No spies ever figured this out, though.