Who Mourns for Adonais? - S2-E2
Continuity mistake: Apollo's lightning bolt throws Scotty across the table and dislodges a big bunch of green grapes from the fruit bowl. They fall onto the table. But when Kirk's crew later assemble at the table, the green grapes aren't there, or in the bowl, or anywhere in the temple. They magically reappear in the bowl just after Spock gets through to Kirk on the communicator. (00:18:55 - 00:41:10)
Continuity mistake: When Losira appears to D'Amato, he looks up from his tricorder, startled. The shot then changes angles, and D'Amato looks up at her all over again. (00:11:55)
Continuity mistake: When Scott orders Sulu to fire phasers to punch through the force field, the two phaser beams are diverging when they leave the ship, but converging somehow (space mirrors?) when they strike the planet. (00:41:20)
Revealing mistake: At the end, a special effects matte flaw causes the rear tip of the starboard side nacelle to vanish briefly as the Enterprise orbits Scallos. (00:45:50)
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)
The Ultimate Computer - S2-E24
Plot hole: When M-5 destroys the ore freighter, Dr. Daystrom says, "Fortunately, it was only a robot ship." But Daystrom wasn't on the bridge yet when Spock announced that fact. He didn't have any way of knowing that the freighter was unmanned. (00:23:00 - 00:25:05)
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.
Other mistake: In this episode, when Kirk's phaser was on overload, it made a small explosion, but in "The Conscience of the King", a phaser on overload would destroy 2-3 decks of the Enterprise.
Revealing mistake: In McCoy's video of the Capellans, the weapon thrown at the sapling actually misses it and nails a nearby bush instead. The tree, however, obediently breaks in half and falls over anyway. (00:00:20)
Continuity mistake: The landing party beams down in daylight, but the window inside Mendez's office shows that it's night outside. In the next exterior shot, it's day again. Next shot back in the office: night. (00:00:30 - 00:05:20)
The Corbomite Maneuver - S1-E11
Continuity mistake: After they've blasted the cube, Kirk and Spock are discussing repairs on the bridge. Spock's earpiece is in place one minute, but vanishes the next when the camera angle changes. (00:13:30)
Requiem for Methuselah - S3-E19
Visible crew/equipment: The monofilament line holding M-4 aloft is visible in the lab when the floating robot delivers the processed ryetalyn to McCoy. (00:17:20)
Continuity mistake: When Kirk splits up the landing party, he asks McCoy to further inspect the vegetation. In the two shot, McCoy isn't wearing his tricorder, but in close-up, it's there, strapped over his left shoulder. Cut back to the two shot, though, and it's gone again. (00:10:20)
Revealing mistake: During the battle scene, the use of special effects stock footage of the view screen, as seen over the helm from the opposite side of the bridge, briefly turns the short, brunette Ensign Chekov into a tall, thin blond guy. (00:44:20)
The Trouble With Tribbles - S2-E15
Continuity mistake: When Kirk is standing in the huge pile of tribbles, he's cradling two large tribbles in his arms in full shots, but only one, and in a different position, in close-ups. (00:40:00)
Continuity mistake: Kirk's arrow strikes the Klingon in the knee. But a few shots later, the shaft is protruding from his thigh, several inches above its original position. Still later, he's holding one hand to his calf just below the knee, which isn't where the arrow was either time. (00:43:40)
The Trouble With Tribbles - S2-E15
Continuity mistake: During the scene when the Klingon agent is exposed by the Tribbles, Kirk first holds the two furballs as if they had a handle on the underside (probably for the parts to make them wriggle). As he turns to Spock (the wide-angle shot), he holds the Tribbles cupped in his hands, his thumbs supporting their flanks. But as Kirk approaches Spock (close-up), he has them 'by the handle' again.
Factual error: Spock says the Klingon ship is approaching at Warp Six, but Sulu counts off the distance at about 50,000 kilometers per second - that isn't even the speed of light.
Other mistake: When the Enterprise hits the Romulan vessel, dust and bricks fall from the ceiling. A starship made of bricks?
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.