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 October evacuated, 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.
The Red October was destroyed, and Jack and Ramius are dead.
- While it's generally chalked up to a botched Chroma Key effect, the translucency of Jack's head during his final conversation with Ramius does lend him a ghostly appearance in several shots. Furthermore:
- The peculiar, multi-plumed explosion seen during the destruction of the Konavalov would make more sense if it were the destruction of two boats rather than one, and the Red October was dangerously (almost suicidally) close when the torpedo hit the Akula. The shock could've easily killed the Red October when the Konavalov went up.
- The fact that they're hiding the sub in a river where Ryan grew up and still harbors cherished memories, a very strange choice strategically, but very much in line with someone's dying mind reaching out for a time and place where the person was happy, or a choice of an afterlife.
- Ryan's flight at the end, unlike his night flight out, is in brilliant light, is glass-smooth, and he's in a peaceful sleep, symbolically suggesting a transition to the afterlife.
Seaman Jones will be on shore assignment with NATO for months
- After all, NATO is now dealing with a new type of submarine stealth drive, and Jones has just invented a way to detect and track it. Obviously, Jones will be busy writing up and explaining his invention to the combined navies of NATO, which will likely start a crash program to modify their marine defences to counter copies of the Red October.