Other than because it's spooky, it's never explained why the heartbeats start up, then stop.
When Spock approaches the two Gideon guards, he uses the Vulcan nerve pinch on the one furthest away from him. Not surprisingly, the guard closer to him sees Spock's hand and reacts. Logically, Spock would have rendered unconscious the man closest to him, and behind his partner, first.
For some reason, as Kirk pages the ship and the camera shows different areas, sick bay and only sick bay is on red alert.
When Kirk arrives on the fake Enterprise, he is standing on one of the pads and is shot from the rear. Then the camera cuts to a shot from the front and Kirk is gone!
When Kirk uses the fake intercom on the fake Enterprise when he first arrives, it doesn't make any noise - later, when Spock arrives and uses it, it makes the standard beeping noise.
Where do the Gideons get their food and water? Their planet is supposedly one huge mass of people - it seems like they'd run out of resources.
The Gideons have long lives, but there's no indication they're super-powered or anything. But Hedin asks his daughter what it's like to feel pain.
The Gideons' plan doesn't make much sense - despite their overpopulation problems they create a huge empty replica of the Enterprise just to fool Kirk for a couple of hours so they can get a blood sample?
How the heck did the Gideons (who are not members of the Federation) get such exact specifications to make what Spock describes as "an exact duplicate of the Enterprise"? Does Starfleet just hand the plans out to anyone?
Hodin: We're trying to readjust the life cycle of an entire civilization.
Kirk: You're killing your own daughter!
Hodin: My daughter hoped to make you feel the agony of Gideon. But it was impossible. No stranger could realize the horror that life can be here. I will not beg for your understanding of my personal grief, nor will I parade it for you to gain your cooperation. My love for my daughter is too deep for display. My pride in her runs even deeper.
Kirk: You're mad!
Hodin: No, we are desperate.
Hodin: What is it like to feel pain? It is like ... when you see that people have no hope of happiness ... you feel great despair ... your heart is heavy because you know you can do nothing ... pain is like that.
Hodin: The people of Gideon have always believed that life is sacred. That the love of life is the greatest gift... we are incapable of destroying or interfering with the creation of that which we love so deeply... life in every form from fetus to developed being.
Hodin: Mr. Spock, you're an officer of a spaceship. In your profession, you use many instruments, tools and weapons to achieve your objectives.
Spock: True, Your Excellency.
Hodin: However, the only tool diplomacy has is language. It is of the utmost importance that the meaning be crystal clear.
Spock: Your Excellency, I am basically a scientist. Clarity of formulation is essential in my profession also.
Hodin: I'm glad to hear it. Perhaps you could then make greater effort to choose your words more precisely.
Spock: We must acknowledge once and for all that the purpose of diplomacy is to prolong a crisis.
Spock: Diplomats and bureaucrats may function differently, but they achieve exactly the same results.
Gene Dynarski also played Ben Childress in "Mudd's Women" and Cmdr. Orfil Quinteros in the TNG episode "11001001."
References the Biblical recount of Gideon. Before Gideon prepared for battle, God told him to reduce the number of his men by having them drink from a stream. Those who drank directly from the stream were sent home and those who scooped water in their hands were kept.
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