In one shot the elevator doors are light gray rather than their usual color.
Just after discussion how DNA is another substance that contracts, Spock turns away to do his calculations and his badge is gone, then flickers back in as he completes his turn.
Just as he prepares to beam down, Kirk describes the spiroid rays as "lethal," but there's no indication that they are, before or after.
It's stated that the bridge crew are beamed away. However, Nurse Chapel is one of the people taken, and she's not bridge crew and given the number of ship's emergency medical situations, is unlikely to have been on the bridge. Also, there are several other people seen on the bridge later who aren't taken as part of the "bridge crew."
As established, when the transporter beams someone down, it immediately restores them to normal size. However, when the Mendent tells Gabler and three other unidentified crewmen that their city is close to destruction, the Enterprise crewmen are still at their miniaturized height. If they had beamed down from the Enterprise, they would be at their normal height.
When Kirk goes to the transporter room to inspect the Terratin city, the macroscope he uses is pointing at an angle toward the floor. However, when he looks through it at the Terratins, the view is if he were at ground level with them.
When Chapel "accidentally" falls into Spock's lap, her collar flickers briefly from black and then reverts to its normal blue.
Kirk forces Harry to give him his last two crystals, but when he throws them into the creature's mouth, there are considerably more. But when they're seen going into its mouth, there are two again.
Spock's insignia appears on the wrong side in one shot as Kirk approaches the rock creature. In the next shot where Spock is in the same position, his insignia is back to the correct side.
During the fight between the two rock monsters, there is a short shot that shows Nurse Chapel, Harry Mudd, Spock, and a unknown red shirted crewman instead of Captain kirk, who should be present.
When Spock and Kirk enter the master computer room, there is a wall behind them about 5'-10' away and no robots. The camera cuts away to the master computer for a second or two, then cuts back to Kirk and Spock and now three robots have appeared between them and the wall. In the next longer shot, the two men are standing in the middle of the room, the robots are behind them, but there's no sign of the wall.
When Uhura is singing by the lake, her reflection in the water doesn't show her uniform rank on her sleeves.
Towards the end of the episode, we see the crew use seat belts. During the original era the Enterprise never before (or since) had seat belts on chairs.
Sulu is shown erroneously sitting on the bridge while he was actually imperiled on the planet's surface.
On the bridge, McCoy's tricorder strap briefly disappears and reappears.
The hangar doors open to the side in this episode, as opposed to from the center like a clam as seen on the original series and later in "Albatross."
Several crew wearing red uniforms have the science (blue uniform) insignia on them.
The episode perpetuates the commonly held belief that witches were burned in Salem. No witches were burned in Salem or anywhere else in the U.S., although some were burned at the stake in Europe.
In this episode the Enterprise explores the center of the galaxy. In Star Trek V - The Final Frontier Kirk claims that no vessel or probe sent into the center of the galaxy has ever returned. (Note however that the Trek producers don't consider the animated series canon.)
The beginning stardate of this episode is 1254.4, which would have it set even before Star Trek's second pilot episode "Where No Man Has Gone Before" at 1312.4. In the latter, Uhura and McCoy weren't yet serving onboard the Enterprise and Sulu was the ship's physicist, and as a science officer, was wearing a blue uniform at the time.