Revealing mistake: When first seen on Gothos, the "frozen" Kirk's eyes blink.
Revealing mistake: As Kirk turns to run on the castle steps, an iron bar barricade appears, blocking his path. When it does, watch the castle wall, and the barricade. It seems to slide just a few inches to line up correctly in the shot, showing poor editing.
Revealing mistake: As Trelane takes a swipe at Kirk, he hits a tree branch. As it breaks away, the building material it was made from is revealed, rather than it being wood.
Revealing mistake: In Trelane's castle, Kirk and Sulu are supposed to be frozen, but they slightly waver.
Revealing mistake: Just before Kirk finds himself in Trelane's "courtroom", look behind Kirk on the bridge above Spock's work station. The viewscreen with the planet on it is actually a piece of paper that's coming away from the wall.
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.