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This is a "Wild Mass Guess" entry, where we pull out all the sanity stops on theorizing. The regular entry on this topic is elsewhere. Please see this programme note.
The Hunt for Red October
Doctor Petrov failing to account for The Mole is due to one of three possibilities
During the film's climax, Captain Ramius orders the Red Octoberevacuated, he orders Doctor Petrov to get an accurate count, so that they do not accidentally leave any crewmembers aboard. Of course, it is later revealed that The Mole is still aboard, which could be due to three possibilities:
The Doctor was incompetent, or at best, distracted, and goofed the count. He failed to realize that he had miscounted the sailors as they disembarked. (Judging from the novel's portrayal of Petrov, this is the most likely possibility.)
The Mole was never included in the official crewcount, meaning that an accurate count would not have revealed him being missing anyway.
Doctor Petrov was also a mole, and knowingly allowed The Mole to remain aboard because he suspected Ramius of being up to something.