Continuity mistake: At the end when the entity left the Enterprise, it came out of the secondary hull, however it left from the engineering dept. The Engineering dept. is located in the back of the primary hull.
Continuity mistake: The first time we see the ship travelling at Warp Nine, it is moving in a level, straight path. Next time, the rear end is elevated above the line of flight. The next time, it's moving in level flight again.
For the World is Hollow and I Have Touched the Sky - S3-E8
Continuity mistake: Natira orders the landing party to kneel before the oracle. Spock does so about a foot-and-a-half to McCoy's left. As the shots change, Spock "jumps" to McCoy's immediate side, then back to his original position, etc. (00:10:35)
For the World is Hollow and I Have Touched the Sky - S3-E8
Continuity mistake: Kirk calls Scott to beam up, and lowers the communicator from his face as he looks at McCoy. In the next shot, he's holding it to his mouth once more. The shot changes one more time, and it's lowered again. (00:31:55)
For the World is Hollow and I Have Touched the Sky - S3-E8
Continuity mistake: After he falls unconscious onto the blue rug, McCoy's position relative to the rug's top edge keeps changing between shots. (00:36:40)
For the World is Hollow and I Have Touched the Sky - S3-E8
Continuity mistake: Kirk orders Sulu to match speed with the asteroid, but in the next external shot the asteroid is closing in on the ship.
Continuity mistake: Sulu's hooded viewer is up as he reports that the Defiant is starting to drift. In the next shot, a reverse angle showing the screen, the viewer disappears. This recurs throughout the episode. (00:06:10)
Continuity mistake: During McCoy's struggle with the orderly, only half of the plastic colored bottles strewn on the table are knocked off onto the floor. But when Nurse Chapel hurries over to tranquilize the orderly, the rest of the bottles vanish, leaving the table completely clear. (00:19:10)
Continuity mistake: When Kirk is being beamed aboard near the end, the crewman operating the transporter has a single lieutenant's stripe. But in the close-up of his hands on the controls, the stripe changes into the braid of a lieutenant commander. (00:46:40)
Continuity mistake: After Spock nerve pinches Chekov when he goes mad and he is taken to Sickbay, the Tholian ship appears and hails the Enterprise. When Spock says "on main viewer," the shot of Loskene is on the screen, but the back of Chekov's head can be seen when it should be in Sickbay.
Continuity mistake: When Checkov turns on the viewer in the transporter room, the Defiant is seen directly from the starboard side, when it should have been seen from the quarter profile port side, as it was drifting to the Enterprise's port side.
Continuity mistake: When Kirk, Bones, Chekov, and Spock go over to the Defiant, the suits they have on have a black support bar in the left side of the headpiece. When the camera looks down at the dead men and back to Kirk, you see the bar is on the right, and his hair is parted on the right. The very next look at Kirk, the bar and the part of his hair is back on the left.
Continuity mistake: The shards of the goblet Spock breaks change quantity and position on the table with the fruit bowl on it. (00:28:30 - 00:31:30)
Continuity mistake: Just before Parmen starts mind-controlling Kirk, McCoy and Spock, he presents them with three gifts. Kirk receives a large, gold Greek shield, which the captain holds with both hands, in front of him, as the lengthy scene continues. In the wide shot, Kirk is holding the shield high up on his chest, completely obscuring his Federation insignia. In subsequent close-ups, Kirk is holding the shield down low, around waist-level, fully exposing his chest and insignia. Every time the camera cuts back to wide-shot, Kirk is again holding the shield up high on his chest.
Continuity mistake: In the 40th Anniversary release of the complete original series, this episode opens with Scotty at the conn, making an extended log entry, wearing his third-season swept-back hairstyle, and it is very obvious that he is visually mouthing several completely different sentences than we hear in the audio. After the opening credits roll, we next see Scotty wearing his more typical relaxed hairstyle with slight bangs. It is apparent that, in remastering and editing this episode, they inserted footage of Scotty from another episode altogether. For whatever reason, it is a glaring mistake of both continuity and audio editing.
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: 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
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: 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.
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.