Plot hole: Scotty is receiving images of the launch, supposedly from an orbiting satellite. But many of the camera views are obviously from ground level, and couldn't possibly have been taken from orbit. It's not a rebroadcast from a ground camera, either. The implication is clearly that Scotty is is picking up a live satellite feed. (00:34:30)
A Piece of the Action - S2-E17
Continuity mistake: At the end of act one, the cue stick standing upright against the pool table just in front of Spock disappears when the view cuts to an overhead shot. It's back again after the commercial break. (00:11:00)
Continuity mistake: In Kirk's log entry, which he somehow makes from jail without a tricorder, he states that 5 witnesses heard him speak to the "spirits." This isn't true, and Kirk ought to know it. The crowd rushed in through an archway after he spoke to Spock and McCoy, and they were all too far away before to hear him. (00:10:50 - 00:26:00)
Factual error: If Miri's planet is a "duplicate" (meaning identical) Earth, it should have clouds. It doesn't. This remains a mistake because "duplicate" means "exactly the same," and thus the clouds should be there. The special effects crew forgot to put them in. Noteworthy: the very first thing fixed in the digitally enhanced version of this episode was the duplicate Earth. It has clouds now. (00:01:30)
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.
Let That Be Your Last Battlefield - S3-E15
Revealing mistake: Due to the use of stock footage once again, Sulu's console viewer appears and disappears repeatedly throughout the episode. (00:08:45)
Visible crew/equipment: In the very beginning, the boom shadow is visible at the top of the screen as Kirk walks to Spock's station on the bridge. (00:00:30)
Continuity mistake: The gash on Kirk's right cheek disappears between the time he and McCoy fall asleep in the cave and when McCoy wakes up to find Kirk at Nona's side. (00:21:30 - 00:23:15)
Other mistake: In the scene near the end when Kirk orders Kyle to beam Hengist into space, Kirk and Kyle say their lines in the wrong order. Roughly: Kyle: Don't get excited, Captain. I would have done it. Kirk: Spock, you do it.
Deliberate mistake: When the decoyed Enterprise heads back to Capella, the special effects shot is reversed to indicate that it's going back in the other direction. Unfortunately, this gives us two brief shots of the ship with the registration numbers backwards. (00:37:40)
Continuity mistake: When Losira comes for Kirk, he's holding Sulu's tricorder with both hands. When the angle changes to include her, he has it in one hand with his right hand at his side. Cut back to a three shot of Sulu, Kirk and McCoy, and Kirk has the tricorder in both hands again. (00:36:55)
Continuity mistake: After Marta's dance, Kirk and Spock are sitting an inch apart behind the table, then a foot apart, then an inch again and so forth every time the shot changes. (00:16:25)
Continuity mistake: When Nona is trying to seduce Kirk, we see a close-up of him with nothing on his shoulders. Cut to a two-shot and suddenly Nona's arms are over his shoulders and around his neck. (00:41:00)
Plot hole: Apparently there is some confusion over the distance between Earth, Starbase 11, and Talos IV. When Spock first meets Pike on Starbase 11 he tells Pike Talos IV is only six days away. Yet when Pike (in the recording) speaks to the Talosians for the first time, he says he is from a star system on the other side of the galaxy. If Talos IV was on one side of the galaxy and Earth was on the other side, it would take hundreds of years at maximum warp to travel from one planet to the other.
Revealing mistake: When McCoy is examining Charlie in sickbay, several shots of the diagnostic panel show a clear reflection of Charlie's upright profile. But Charlie isn't sitting up during the exam - he's lying flat on the table. The close-ups of the panel were shot while actor Robert Walker Jr. was either sitting or standing nearby. (00:04:10)
Continuity mistake: Gary Seven is talking to his computer, we then switch to Kirk and Co and after a few moments with them we cut back to Gary Seven. Somehow in that time, while talking to his computer he changed his clothes. (00:13:40)
Plot hole: Spock claims that history is unchanged at the end of the episode according to the library tapes - how would he know? If history changed, the tapes would change too. And unlike in "City on the Edge of Forever", there's no Guardian around to keep people from being influenced by an altered timeline.
The Trouble With Tribbles - S2-E15
Continuity mistake: When Kirk and McCoy dispute about the tribbles on the Enterprise bridge, Kirk holds the two tribbles in his hands at alternate heights. In the shots where McCoy's face is seen, he holds them next under his chins, but when Kirk's face is seen, he holds them at chest level.
Space Seed - S1-E23
Plot hole: It is stated during the episode that Khan was, at one time, the ruler of over 1/4th the Earth's population, during a very key moment in the planet's history (The "Eugenics" Wars). Such a personage undoubtedly would be very well known to 23rd century Earth people, at a level of infamy approximating Julius Caeser or Adolf Hitler. Yet it is only 2/3rds the way through the episode, thanks to a computer search by Spock, that the crew divines his identity. Lt. McGivers at the very least should have almost instantly recognized him.
Continuity mistake: When Sarek enters the banquet room to take his medication, the Tellarite sitting at the table holds a glass in his right hand. In all the full shots with Sarek in the foreground, the glass switches to the Tellarite's left hand. In all the close-ups of him, it's back in his right again. (00:14:50)
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.