Somehow, just before Spock is being beamed back to the Enterprise, the Romulan Commander hears the transporter sound effect and quickly gets in proximity to him, getting beamed away with him. However, the sound effect is usually heard at the same time the transportee begins to vanish, not before.
There seems to be no reason for the Romulan Commander to believe Kirk is still aboard the Romulan ship with the cloaking device. For one thing, he uses the transporter to escape and that should have been detected. Even if it wasn't, why would she believe the intruder was still on the ship? Instead, she seems to assume the thief is still on the ship and wastes time searching.
Kirk rather handily disposes of two Romulan guards, with a single punch and later a single kick. It's hard to imagine him knocking out Spock so readily, compared to these trained warriors.
Given the two Romulan officers beam aboard as hostages, there seems no reason for them to instantly draw their guns. Or even come aboard armed.
When Tal gives them one hour to consider surrender, there's an odd reverb effect to his voice that is not present previously, and for which there is no on-screen reason.
It seems improbable that the Enterprise, surrounded by three Romulan vessels, would be able to make a run for it without instantly being fired upon by the surrounding enemy vessels.
When Spock is making his final statement, the Romulan Commander states that his 20 minutes are almost up, though he started only moments before.
It seems odd that the Romulans, who were once part of the Vulcan race, are unaware there's no such thing as a "Vulcan Death Grip." By many sources, they left Vulcan because their cousins were too peaceful. Odder still, Nurse Chapel does know there is no such thing as a VDG.
When the Romulans call Kirk to have him transport over, Kirk looks directly into one of those tri-screen displays in the briefing room. Because of the way he looked he shouldn't be able to see the Romulan, or the Romulan see him.
Captain Kirk lets the (enemy) Romulan commander onto the high-security classified bridge in the middle of a battle.
When the Enterprise was escaping at the end, the space sensor array was off.
Spock and the Romulan Commander travel from deck 1 (the bridge) to deck 2 (her temporary quarters), but they spend several minutes on the turbolift doing so. Deck 2 is the science level. They should have gone to deck 4.
The Romulan Commander believes that Spock is trying to steal the cloaking device. So she hauls him down to the room holding it, goes into the room, and looks pretty much everywhere except the spot where it was mounted - doesn't she know where the device is. Finally her sub-commander tells her that it's gone, and she turns around and sees the empty slot.
At the end, the Enterprise had only the left warp nacelle.
Kirk: The design of the ship is the same. Mr. Spock? You said you had a theory on why your sensors didn't pick up the new ships until they were upon us.
Spock: I believe the Romulans have developed a cloaking device which renders our tracking sensors useless.
Kirk: If so, the Romulans could attack into Federation territory before we would know they were there. Before a vessel or a planet could even begin to get their defenses up.
Scott: They caught us right enough.
Kirk: Well that's a brilliant observation, Mr. Scott. Do you have any other helpful opinions?
Romulan Commander: There is no force I could use on a Vulcan that would make him speak. There are, however, methods that are completely effective against humans, and human weaknesses.
Spock: They would prove ineffective against the Captain.
Romulan Commander: Then they will leave him dead, or what might be worse than dead.
Uhura: Doctor, beam aboard the Romulan flagship immediately. There's been an injury.
McCoy: I don't make house calls.
Romulan Commander: Is my attire now more appropriate, Mr. Spock?
Spock: Commander, your attire is not only more appropriate, it should actually stimulate our conversation.
Romulan Commander: Mr. Spock. You do know I have a first name.
Spock: I was beginning to wonder.
Romulan Commander: Well, I do. Would you like to hear it? (she whispers)
Spock: How rare and how beautiful. But so incongruous when spoken by a soldier.
Romulan Commander: If you will give me a moment, the soldier will transform herself... into a woman.
McCoy: (to Spock, after Kirk is rendered unconscious) What did you do? What did you do?!?
Spock: I was unprepared for his attack. I instinctively used the Vulcan Death Grip.
McCoy: Well your instincts are still good, Mr. Spock. The Captain is dead!
Romulan Commander: You must have your own ship. I will see to that if you will stop looking on the Federation as the entire universe. It is not, you know.
Spock: That thought has occasionally crossed my mind.
Romulan Commander: I have heard of Vulcan integrity and personal honor. There's a well-known saying--or is it a myth--that Vulcans are incapable of lying?
Spock: It is no myth.
Romulan Commander: Then tell me truthfully now, by your honor as a Vulcan, what was your mission?
Spock: I reserve the privilege of speaking only when it will not violate my honor as a Vulcan.
Romulan Commander: It is unworthy of a Vulcan to resort to subterfuge.
Spock: You are being clever, Commander. That is unworthy of a Romulan.
Romulan Commander: I hope that one day there will be no need for you to observe
Spock: It would be illogical to assume that all conditions remain stable.
Romulan Commander: Romulan women are not like Vulcan females. We are not dedicated to pure logic and the sterility of non-emotion. Our people are warriors. Often savage. But we are also many other pleasant things.
Spock: I was not aware of that aspect of Romulan society.
Romulan Commander: As a Vulcan, you will study it. As a human, you would find ways to appreciate it.
Spock: Please believe me. I do... appreciate it.
Romulan Commander: I am so glad.
Romulan Commander: Oh, you must be mad.
Spock: I assure you, I am quite sane.
Romulan Commander: Why would you do this to me? What are you that you could do this?
Spock: First officer of the Enterprise.
Spock: It is regrettable that you were made an unwilling passenger. It was not intentional. All the Federation wanted was the cloaking device.
Romulan Commander: The Federation? And what did you want?
Spock: It was my only interest when I boarded your vessel.
Romulan Commander: And that's exactly all you came away with.
Spock: You underestimate yourself, Commander.
Romulan Commander: You realize that very soon we will learn to penetrate the cloaking device you stole.
Spock: Obviously. Military secrets are the most fleeting of all. I hope that you and I exchanged something more permanent.
Romulan Commander: It was your choice.
Spock: It was the only choice possible. You would not respect any other.
Romulan Commander: It will be our secret.
McCoy: You're due in surgery. I'm going to bob your ears.
Spock: Captain, please go. Somehow, they do not look aesthetically agreeable on humans.
McCoy: Well, are you coming down or do you want to go through life looking like your first officer?
Kirk: I'm on my way!
In the Remastered Edition of this episode, the three Romulan ships surrounding the Enterprise are two designed like the Klingon battle cruiser and a single Romulan Bird of Prey. The Klingon-style ships bear the Romulan Bird of Prey insignia on their ventral side.
Features the first appearance of the Klingon battle cruiser. The Romulans were using this ship so the producers could save on the cost it took to actually build the cruiser. [Editor's note: Technically, "Elaan of Troyius" (#60043-57) featured the first appearance of the Klingon battle cruiser since it was made before this episode. (#60043-59)]