The Empath - S3-E12
Continuity mistake: During Kirk's torture scenes, the back shots have Kirk's arms stretched wide apart and yanked straight - the front shots have the chains going overhead and his arms are bent at the elbows.
The Empath - S3-E12
Continuity mistake: In the opening scene inside the underground station, the bright blue mat under the viewer desk chair disappears. (00:00:55 - 00:02:30)
The Empath - S3-E12
Continuity mistake: After partially healing him, Gem falls away from McCoy and lands, unconscious, perpendicular to the dais he's lying on. When Kirk and Spock rush over, however, she's suddenly moved several feet away and is now lying parallel to the dais. (00:44:50 - 00:45:35)
The Empath - S3-E12
Continuity mistake: The bruises on McCoy's face change configuration, color and texture between the time Kirk and Spock first find him and the scene where Gem heals him. (00:34:15 - 00:40:30)
The Empath - S3-E12
Continuity mistake: Gem's left hand is cupped around McCoy's right ear as she begins to heal him, but her hand keeps changing positions as the camera angles switch. (00:44:20)
The Empath - S3-E12
Revealing mistake: When the Vian fires his weapon at Kirk after the crew finds Gem, Kirk flies backwards. At this point, Kirk is not William Shatner but a stunt double.
The Empath - S3-E12
Plot hole: Spock calculates that it will take 72 hours for the solar flare to pass, and Kirk orders the Enterprise out of the area. 3 days is a long time to go without food or water, and as the station is deserted as far as they know, there'd be no way to supply themselves, but the Enterprise leaves without a second thought.
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.