Continuity mistake: When Kirk informs Galileo that all systems are clear for takeoff, in the shot from inside the shuttlebay as Galileo turns to launch, the shuttlecraft Columbus is also in the hangar deck, but when Galileo exits Enterprise the Columbus is gone in the exterior shot. (00:01:45)
Continuity mistake: In the first scene when Spock is piloting the shuttle craft out of the Enterprise and into space, as the bay doors open you can see both the ship's shuttles, the Galileo, and right behind it the Columbus. Yet as soon as the Galileo clears the bay doors, in the immediate reverse shot, the bay is empty and the Columbus has disappeared. (00:01:45)
Continuity mistake: After Spock tells Boma and Gaetano that he's in command and they should fire only to frighten, not to kill, one of the creatures throws a spear and then his shield at the trio, and when the shield hits the ground it's much smaller than the huge shield lying on the ground in the next close-up. (00:23:15)
Continuity mistake: As Kirk speaks with Commisioner Ferris, Kirk's hands go from holding a piece of equipment to being straight down by his side, back to holding the equipment.
Continuity mistake: Latimer falls down face down but when picked up he is already face up.
Continuity mistake: While Kirk questions Spock about his command decision on the Galileo, shots of Uhura and Mears show the ladies close together at Uhura's station with Mears' hands hidden but close up shots of McCoy show Mears and Uhura in the background further apart from each other and Mears' hands in front of her body.
Continuity mistake: As the Galileo re-enters the atmosphere, you can see Scotty in the copilot chair. His hair is parted on the left side, but in the interior shot, it's parted on the right.
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.