Other mistake: Kirk and Spock stun two Klingon guards, yet despite being unconscious, the guard on the left jumps from the balcony and lands feet first on the ground. If he were really unconscious he would have simply tumbled down. (00:36:20)
Continuity mistake: The Organians cause all the weapons to overheat, and everyone drops them to the floor. When Kor moves to the desk to call his ship, though, he's wearing his disruptor. It's gone again when he returns. (00:41:45)
Visible crew/equipment: After the Klingon vessel's attack on the Enterprise, while returning fire just as Kirk orders to maintain firing range at 100% dispersal pattern, the set's unfinished wood plank with grey paint drip marks can be seen at the bottom of the screen. Additionally, at the end when Spock goes to stand beside Kirk's chair (also when he walks away) the actor's mark can be seen on the floor by Spock's feet.
Visible crew/equipment: When Kirk is thrown into jail with Spock you can see the movement of the entire blue crash mat used to break his fall.
Continuity mistake: When Kirk orders the crew to fire phasers; the exterior shots show the ship firing torpedoes, and torpedo explosions flashing out in space.
Factual error: When Kirk/Spock enter/leave the Council Chamber, the doors quietly open unaided (as though there were motion detectors in operation), yet the Organian culture - determined by Spock to be approximately Class D minus on Richter Scale of Cultures - would not have had such technology. A fact overlooked by Kirk and more importantly, Spock.
Character mistake: When Kor describes the effects of the mind-sifter to Kirk (who is still in disguise as an Organian), he says the machine would leave him "more vegetable than human." There is no reason a Klingon would reference humans while speaking to a person he believed to be Organian.
Other mistake: When Kirk is lecturing Ayelborne in the council chamber, the actor behind him is mouthing Kirk's dialogue.
Continuity mistake: Kirk has a sunburn on his face and chest (it appears to end partway down his chest-most noticeable in the scene shortly after his identity is revealed to the Klingons). First of all, how does one get a sunburn while flying through space (and one that does not match the pattern of the uniform). If one wants to explain it away as being from a recent Shore Leave or Enterprise tanning bed, the issue still remains that the intensity of the sunburn changes as the episode continues.
Deliberate mistake: When the Klingons post signs for their rules, they're printed in English. The Klingons have their own language, and people on Organia most certainly aren't English speakers. Even if the Universal Translator allows Kirk and Spock to hear in English, it wouldn't change the look of a sign.
The Alternative Factor - S1-E28
Continuity mistake: Both the positive and negative versions of Lazarus have a long mustache and a fairly full "waterfall" beard - until the scene in the briefing room, when inexplicably, the mustache and beard are both suddenly so thin they're barely visible. As soon as they beam down to the planet, however, the much thicker facial hair is restored. (00:23:00 - 00:24:30)
The Alternative Factor - S1-E28
Continuity mistake: Lazarus had knocked out the transporter technician, but when Kirk arrives he is fine and operating the transporter. (00:37:35)
The Alternative Factor - S1-E28
Continuity mistake: Mad Lazarus has just put a black-and-white hatch cover over the stolen dilithium crystal in his time ship. It's in place when Kirk arrives to confront him. But a moment later, when Kirk leans in and is accidentally transported to the negative universe, the cover has disappeared. It's still missing when Kirk returns to push Lazarus through the portal. (00:39:20)
The Alternative Factor - S1-E28
Continuity mistake: Kirk keeps referring to Masters as "Lieutenant", even though she has no braid on her sleeve - all Enterprise lieutenants have a single gold braid on each sleeve.
The Alternative Factor - S1-E28
Plot hole: Kirk knows that Lazarus is insane and that he wants the Enterprise dilithium crystals. Yet he's not restrained in sickbay and is, in fact, given free run of the ship so that he can knock out the crew in engineering and steal the crystals. Other than to further a woefully weak plotline, this makes no sense whatsoever.
The Alternative Factor - S1-E28
Continuity mistake: Lazarus' goatee and facial injures are constantly changing.
The Alternative Factor - S1-E28
Other mistake: When Spock calls Kirk to the bridge after he discovers the Lazarus energy source, he and Lazarus head to the bridge. There is a shot of McCoy standing in the corridor, and one of the red alert panels is burned out while the other is still flashing.
The City on the Edge of Forever - S1-E29
Continuity mistake: While he and Kirk discuss the history tapes in their room, Spock's shirt collar is turned up on the left side in close-ups, but straightened out in the full shots. (00:32:55)
The City on the Edge of Forever - S1-E29
Continuity mistake: After Edith stumbles and nearly falls down the stairs, she still has both her shoes on. But after the kiss, she proceeds up the stairs and is now carrying one shoe. She had no time to take it off, as she was, er, busy with Kirk the whole time. (00:43:55)
The City on the Edge of Forever - S1-E29
Factual error: This episode takes place in NYC during the 1930's, but after McCoy's phaser is stolen in the exterior shot of the buildings a fallout shelter sign can be seen. These signs were put up no earlier than 1961.
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.