Continuity mistake: When Nomad first appears on the bridge, the indicator light on Scott's communicator panel is on. A second later, it's off, and he turns it on to say his line.
Revealing mistake: A number of times through the episode, the wire holding Nomad up and moving it around is visible. Example: When Nomad first moves off the transporter pad, look directly above it; the black wire can be seen in front on the light over the pad.
Continuity mistake: As Nomad first hears Uhura's singing, it extends antennae and leaves the room. After a quick cut scene, as it turns in the corridor the antennae is retracted, then out again on the bridge.
Visible crew/equipment: When the camera looks at Spock after Scott's body is removed from the bridge, the shadows of lighting equipment is visible behind him.
Continuity mistake: When Scotty awakens in the sick room after being attacked by Nomad, Nurse Chapel has her hands placed on him. In the next shot, when McCoy tells Scotty to take it easy, Nurse Chapel's hands are no longer on Scotty, and in the next shot, her hands are back on him.
Revealing mistake: When Kirk, Spock and McCoy study a diagram that shows various parts of the Nomad probe, the lower right of the diagram reads "Computer Data Banks Recall & Transmition". It should read "Transmission".
Continuity mistake: When the security team is escorting Nomad back to the holding area, he goes his own way. One of the team then says, "Hey Nomad!" and begins to reach for his phaser. But in the next shot, he has already got his phaser out and trained on Nomad.
Continuity mistake: When Kirk sits down to consult the computer, the big green potted plant on the shelf behind him is there in full shots and missing in close-ups. It's much too large to be completely hidden behind him: if it shows up behind his head in full shot, it should show in close-ups, too, but it doesn't. It's not there. (00:16:30)
Visible crew/equipment: When McCoy gives the guard a shot and he and Scotty break into Engineering, you can see a crew member's hand holding a red handle and their bare arm (it's not Scotty), who apparently is helping to open the door. (00:23:00)
Continuity mistake: Kirk punches the Imperial crewman that helps him in the face, but when the guy falls on the ground he's holding his side.
Continuity mistake: A subtle mistake, but when Spock is lying on the table in sick bay and recovers, the readings on the monitor are in the normal range. However Spock, as a Vulcan, produces very unusual readings on the monitors in other episodes.
Revealing mistake: During the fist fight between the transported crew and Spock, the use of stunt doubles in the wide shot is quite obvious.
Continuity mistake: As there were two screen used models of the Enterprise, when the ship is seen flipping from one universe to the other and back, the nacelles of the Imperial Enterprise have the solid red fronts with what appear to be antennae.
Continuity mistake: As Kirk and party dematerialize, Kirk's arms are by his side. As they are briefly seen in the Transporter room, his left hand is up with the communicator.
Revealing mistake: In the close up shots of the mirror Sulu, the poor make up job of the scar on his face is very evident.
Continuity mistake: At the end, Lt. Moreau gives Kirk a report to sign. After signing and giving it back, and after a dialog with Spock, he gets up, goes to Moreau, has the report and looks at it again.
Continuity mistake: Throughout the entire episode the planet's sky is red, yet during the scenes where the clouds come and lightning strikes, it becomes obvious that they simply used stock footage of Earth's clouds, since the sky is blue. (00:11:50)
Visible crew/equipment: When Vaal is not fed and he starts spewing smoke everywhere, you can see a volcano type firework going off just inside his mouth. (00:43:55)
Answer: Kirk was getting his physical and Dr. McCoy probably turned off communications, because if he hadn't, Kirk would have left and headed straight for the bridge, leaving McCoy irritated.