Continuity mistake: The shots of the rocket Scotty cycles through are of different times. There is one shot of the rocket at the launch site, followed by one of the transport taking the rocket to the site.
Continuity mistake: As Kirk talks to Chekov on the screen, his hands are flat on the table, and there is a collection of data tapes in front of him. After the angle change, his hands are clasped on the table, the tapes have been replaced by a data pad, and Kirk appears to be frozen.
Revealing mistake: "Trek's" new 3rd season uniforms were tighter-fitting than their velour predecessors, presenting a problem for some actors. When the landing party beams down in this episode, the outline of William Shatner's tummy-wrapping girdle is very visibly showing through his costume. (00:13:10)
Continuity mistake: When Kirk and his landing party beam down to the planet there are six shots of Morg, who have their right arms covered in fur in all those flipped shots, but when Morg attack the landing party it's their left arms covered in fur. Presumably, the first six shots were flipped for direction continuity. (00:13:15)
Revealing mistake: After Kirk and the crew arrive underground, he stuns Kira and removes her bracelet. After he removes it, the unconcious woman quite deliberately lays her hand flat on the ground. (00:21:15)
Continuity mistake: When Kara renders the landing party unconscious, Kirk falls with his arms splayed out to each side. But in close-ups, he has one hand folded over his chest. (00:23:30)
Revealing mistake: It would seem that with the incredible advanced knowledge and furnishings that have been bestowed upon the Imorg down below, the 'Teacher' should have at least provided them with adequate high tech structuring and not the ratty, torn and warped substandard sheet rock seen on the bottom of the walls in these two camera shots. Yep, they can remove and restore a brain but can't find a place to buy good quality plasterboard. (00:23:40 - 00:33:51)
Continuity mistake: When Scotty, Kirk, and the others follow Spock's signal to the chamber with the Controller, they encounter Kara and she activates their pain bands. Spock's body has a pain band around his waist as the other men drop to the ground, but after McCoy tells Kirk, "Spock, no pain," the pain band is missing from Spock's body, then in the next shot it reappears when he goes after Kara's bracelet. (00:35:05)
Continuity mistake: After Spock's Brain is taken McCoy says he has no idea how long the body can last on life support without the brain. Somehow in the following few moments McCoy has established that Mr Spock's Body will die in exactly 24 earth hours. No explanation is given as to how he came up with this figure.
Continuity mistake: In the beginning Chekov disappears off the bridge for a moment and is replaced by a blond haired crew member, then he returns.
Factual error: In the opening sequence, Spock identifies the alien ship as possessing "ion propulsion" which he says is "unique technology." Scotty is similarly impressed and says, "They could teach us a thing or two!" Kirk later comments that "Advanced ion propulsion is beyond even our capabilities." However, even back in the 1960s, ion propulsion was physically feasible, while Warp propulsion was complete fantasy. Ion propulsion of any kind could never even reach lightspeed and would be incredibly primitive compared to Warp technology. In fact, we in the 21st Century have already developed ion propulsion, but it will probably take many hundreds or thousands of years to develop anything even close to Warp technology.
The Enterprise Incident - S3-E2
Audio problem: During the scene where Kirk is talking in the briefing room, the director was obviously not pleased with how James Doohan said his lines. Due to budget constraints, instead of re shooting the scene, they simply replaced Mr Scotts dialogue with another one. You can see it since at one point his lips are completely out of sync, even on the remastered edition. (00:06:40)
The Enterprise Incident - S3-E2
Other mistake: When Chapel comes into Sickbay and looks at the "dead" Captain, the camera goes to close up of Kirk, and he wakes up. After she yells for McCoy, the camera goes back to Kirk, and he goes back to sleep. The motions of him waking are obviously played in a slow reverse instead of him quickly closing his eyes.
The Enterprise Incident - S3-E2
Plot hole: In the conference room, Spock informs Kirk that his theory of a Romulan cloaking device kept the sensors from detecting the ships. However, in S1:E14, "Balance of Terror", they figured out the cloaking device, and how it worked. Unless he was feeding into the deception, Spock shouldn't have had any theory when it was a fact.
The Enterprise Incident - S3-E2
Plot hole: Despite the Romulan ships keeping a close watch on the Enterprise, when they beam the disguised Cpt Kirk over to the Romulan vessel it goes undetected.
The Enterprise Incident - S3-E2
Continuity mistake: When the guard opens the cell barrier, the light bars turn off, then slide back. As they come back out, they're already on, rather than the reverse of the opening procedure.
The Enterprise Incident - S3-E2
Other mistake: As the Romulan commander goes to answer the intercom, the switch she touches to open the link is already on, probably left that way from a previous take.
Factual error: Mr. Spock states that the asteroid is almost as large as the Earth's Moon. Such big bodies must be predominantly spherical due to their own gravity. However, the asteroid is very elongated, with a very irregularly shaped surface. (00:06:40)
Continuity mistake: When Miramanee and her companion first see Kirk at the obelisk, the two women are standing, holding their fruit baskets, just inches from each other. In the very next, reverse angle shot, they're suddenly several feet apart. (00:09:10)
Factual error: When Kirk is given the medicine badge, it's a stretchy elastic/Spandex headband. This is supposedly a completely pre-industrial culture paralleling the early Native American tribes. They have no fabric, no yarn, no spinning wheels - only hides and animal hair, neither of which can stretch a la Spandex. (00:14:40)
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.