When the landing party reaches The Controller's room, Kara inflicts pain with the belts that had been placed on them earlier. McCoy drops the device that controls Spock's body, and Kirk painfully reaches for it. When the camera angle changes, Spock's body is not wearing a pain belt. When the angle changes again, Spock is once again wearing a belt.
The opening scene on the bridge from behind shows Sulu in the helmsman's chair and a tall blonde person in the navigator's chair. A few seconds later it shows Chekov in the navigator's chair.
The "star date" starts on 5431.4 but in mid-show the date is inexplicably given as 4351.5.
The planet in question has repeatedly been labeled as "Sigma Draconis 6," but when in the lair of the Eymorg, Kirk's log entry refers to it as "Sigma Draconis 7." Sulu's subsequent log entry also refers to the planet as "7."
Just after Dr. McCoy connects Spock's finger, wrist and elbow, a closeup shot of Spock's face shows he has no make up on. After the operation Spock is talking and a closeup shot shows his face properly made up.
After McCoy has reinserted Spock's brain through complex surgery on his scalp, Spock sits up with a full head of hair, with no sign that any surgery has taken place.
After Dr. McCoy reattaches Spock's brain, Spock springs up and congratulates McCoy. There are no signs of any surgical scars on Spock's head. However, the technology avaialable (including devices like the anabolic protoplaser and the dermal regenerator) allows surgeons to heal lesions or incisions without leaving scars and to remove pre-existing scars.
When the Morg first approach the landing party, they have fur sleeves on their right arms. When they meet the landing party, the film is reversed and the fur sleeves are now on their left arms. The fact that the fur sleeves are on the left arms when they meet and interact with the landing party indicates that the early scenes where the Morg are seen alone, and are sneaking up on the landing party, are the scenes that are reversed.
The Morg are supposedly a primitive, almost caveman-like species, yet the seams on their clothing are perfectly stitched. How are they able to stitch such perfect clothing if they haven't even progressed past the stone age and haven't learned to use iron?
The "male-female schism" explained in the story line simply does not make sense from a biological point of view. Men are shown to have no knowledge of women, yet somehow the species is able to reproduce and it is implied that the women kidnap men to be mates in their world under the planet's surface. This fails to explain how the male population on the surface sustains itself, given that males would have to be born from a mother, raised to a certain age, and then "released" back to the surface, which seems to defeat the purpose of capturing men in the first place and bringing them below to the women.
Granting that with the right technology it would be possible for Spock's disembodied brain to be able to speak as it does to the landing party. However, there is no way for it to do so with Spock's own voice. The brain, being disconnected from its body, would have no access to his vocal chords. Any voice would have to be synthetic in nature.
If the library of the Old Knowledge was so advanced as to be able to give the user the knowledge to be able to safely remove and transport a Vulcan brain, and provide an environment where the brain could survive, it almost certainly would have been able to provide the knowledge necessary to build an electronic controlling computer capable of performing all the tasks Spock's brain was performing.
Sulu commits a mild breach of military protocol during his log entry by referring to Spock, a superior officer, as "Spock" without any title or honorific.
After operating on Spock's brain, Dr. McCoy refers to "joining gangula", he almost certainly meant "joining ganglia" - not an error a medical professional would make.
At approximately 13:05, Kirk says "Suit temperatures to 72". This implies that the uniforms have environmental controls, a notion not supported anywhere else in the entire Star Trek franchise.
Nurse Chapple professes her undying love for Spock throughout this series. She is very unemotional at the sight of Spock lying on the bio bed brainless and on complete life support.