Stupidity: Reliant's prefix code is 16309. This code prevents an enemy ship from ordering a friendly ship to lower its shields or something similar. Five digits with no symbols. We know that symbols and letters aren't used since Spock uses a 10 digit set of switches to input the code. This is ludicrous. In 2016, a high powered server could crack a 6 digit password in approximately 0.0224 seconds (at 100 billion guesses/second). Any starship computer would have to far more processing power then a 2016 server. The prefix code protecting a starship from cyber attack would have to be insanely complex in order to be useful.
Plot hole: Why doesn't Reliant know that Khan is exiled here? The Federation is so terrified and opposed to genetic engineering that it's still illegal 300 years after Khan. So why is there no warning along with the data on the Ceti Alpha system? Kirk logged what happened with Khan and his solution of marooning him. Starships use nav data to navigate star systems. Ceti Alpha 6 exploded, yet the helmsman or computer never noticed that there is one less planet than there was when Kirk was there? There is no debris from the explosion? Ceti Alpha 5 is the exact same size and was conveniently blown into the exact same orbit as Ceti Alpha 6 used to have? So there is nothing whatsoever to make the crew even suspect that it's not 6? Enterprise would have to have scanned the planets in the system to know that one was habitable for Khan. Did Ceti Alpha 6's destruction somehow magically turn Ceti Alpha 5 into its exact duplicate? If Starfleet ships have been there to map after Ceti Alpha 6 exploded, none of them bothered to check on the exiles? Pretty callous for Starfleet, don't you think? With the technology and amounts of information available to Starfleet vessels, there is NO logical reason for the Reliant to think that this planet is Ceti Alpha 6. Finally, would the Federation be willing to test a device whose exact effects will be unknown on a planet so close to another inhabited one? (00:21:00)
Trivia: Early script drafts featured Khan gaining psychic powers with the ability to create illusions in the minds of others. One draft even replaced Khan entirely with an original villain who better suited such fantastical mental powers. By the time Nicholas Meyer wrote the shooting script, Khan was reinstated as the villain and the psychic angle was dropped.
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