When Kirk first sees Sulu and Scott in the dungeon, Sulu walks ahead of Scott. Camera cuts to Kirk but when it cuts back a moment later, Sulu is behind Scott.
At the end of the opening scene, Spock accompanies Kirk into the turbolift, presumably to go to the transporter room with him. But Spock is not in the transporter room scene that follows.
When Kirk is alone with Sylvia, several close-ups of Korob show him spying on them from behind the screen (behind the throne/chair). However, when the scene shows Sylvia (with the screen in the background), Korob is not there.
Near the start, when Kirk is trying to reach the landing party, he leans over Uhura to use the control panel. In the next shot, he appears to be standing up straight.
When Kirk goes back for the transmuter, Scotty's position changes from when he was rendered unconscious by Spock a few moments earlier.
Once a skeleton's connecting tissue has decayed, the skeleton falls apart unless the bones are wired together to maintain its shape for display. The skeletons seen in the dungeon would actually have been just piles of bones on the floor, not hanging in chains and the cage.
The black cat is a short hair in some shots and a long hair in others. This is presumably part of the shape-shifter's abilities, although it was probably really just a goof.
While in the dungeon, Spock mentions something about Jackson just before he collapsed. Spock was not present when Jackson collapsed. However, there were many opportunities when Spock could have been apprised of the situation.
Obvious wig on Chekov (see trivia).
When Kirk fights McCoy, McCoy's weapon falls to the ground and bounces showing that it is made of rubber.
The skeleton in the dungeon has a hinge on its skull, showing that it is not real. Probably a educational model skeleton.
When McCoy steps onto the rocks at the end, they wobble under his feet.
After Kirk, Spock, and McCoy first enter the castle, and the black cat runs away, there is a three-shot of Kirk, Spock, and McCoy. At this point, Kirk's trigger finger appears to pull the trigger on the phaser twice, but nothing happens.
The three witches dressed in black early in the episode were more than heads floating in space. It is clear as the sequence advances that the witch on the far left is wearing a dress. The other witches are similarly dressed but not as apparent.
The initial landing party makes no sense. Kirk almost always leads the landing party himself. The planet is seemingly uninhabited and has sparse plant life. If he doesn't go himself, he would send Spock with a team of professional scientists with a heavy concentration in geology and meteorology. Instead, Kirk sends an engineer, an amateur botanist, and a command-track officer. Not a blueshirt in the bunch.
Throughout the series, Spock prides himself on his knowledge of Earth history. It's odd that he never heard of the custom of 'trick-or-treat', although it is possible that this practice has largely died out and has become obscure. Given what Star Trek history maintains happened in the 21st century wars, the custom of sending children to knock on neighbors' doors would surely have disappeared.