The position of the landing party changes when the "mirage survivors" disappear.
When the Enterprise's landing party first beams down to Talos IV, the man on the far right has his left hand on the strap of his backpack in the transporter room, but when he materializes on the planet's surface, both of his hands are on the silver object held in his right hand.
When the landing party is about to step onto the transporter pads, to beam down to Talos IV, one of the transporter technicians is wearing spectacles, with thick lenses and black rims. In the next shot, he is not wearing them.
As Pike retreats up the stairs from the warrior on "Rigel VII", you can see the blade of his spear bend as it pushes against the warrior's chest.
When Captain Pike is abducted, remaining crew members fire a barrage of phaser weaponry at the portal; in each of the three attempts, the exact same effect results. Parts of the entryway get blasted out, and then with each succeeding blast, the exact same thing happens to the "door." In addition, though one of the crew fires his phaser from a different location than Tyler and Spock, his shot appears to be coming from the same location as Tyler's.
When Spock and Tyler are firing at the entry way, Dr. Boyce is standing beside them (only his left side visible ) standing casually with his arms behind his back and looking somewhere ahead of him. (John Hoyt probably didn't realize he was in the shot.)
The bed in Pike's quarters was far too short for Jeffrey Hunter. His feet are extending well beyond the end of the mattress, as he briefly reclines on it.
The view of the Enterprise supposedly in orbit appears to be traveling through space.
The sound of The Keeper's voice constantly changes. This is because the video was put together from footage used in "The Menagerie" using Vic Perrin's voice, and 'rediscovered' footage with Malachi Throne's voice. Vic Perrin was used to dub the keeper in The Menagerie: Part I (1966) and The Menagerie: Part II (1966) because Malachi Throne appeared in The Menagerie in person as Commodore Mendez, and the voice would have confused viewers. Originally, the whole of "The Cage" used Malachi Throne's voice for the keeper.
Wooden batons, nailed to the rock outcrop on the barren planet, to allow the actors to walk up the slope, are clearly visible.
When Pike fires the apparently non-operational laser weapons at the transparent divider, he fires once with the first laser and twice with the second. He wagers that the Talosian is keeping him from seeing that the weapons did in fact burn through the transparent divider. If that was the case, however, the wall outside the cage should be scorched by the subsequent shots, yet it appears intact and unmarred.
The Talosians wanted to attract a mate for Vina "to perpetuate the species", but this would be impossible with only two people. A minimum of about 200 would be needed in order to have a sufficiently diverse gene pool.
Vina is revealed to be old and handicapped, with only an illusion of a beautiful young woman projected over her true appearance by the Talosians. Yet when Pike, Colt, and Number One make their escape from the cage and to the planet's surface, she is able to keep up with them with no difficulty, something someone in her condition should not have been able to do.
When Captain Pike and Dr. Boyce meet in Pike's cabin, Pike clearly says: "Unless we get anything more positive on it, it seems to me the condition of our own crew takes precedent." "Precedent" is used incorrectly. The word should have been "precedence".
The Talosians wish to use Pike and one of 3 human females to propagate a servant class. The human from the original crash, Vena, was one of the 3 options. However, she was revealed to have been an adult when the ship crashed 18 years earlier. She would be well past her prime child-bearing years by the time of these events, even if she was in good enough health after the crash to produce children (highly questionable given her physical state).
When the phaser cannon being used to breach the Talosians stronghold begins to overheat, Number One uses her communicator to call up to the starship Enterprise (which is supplying the power) and order them to "disengage." When the cannon continues to fire, she lowers the communicator, looks up, and YELLS "Enterprise, disengage!" to the orbiting ship.
Pike complains about Yeoman Colt, saying that he "can't get used to having a woman on the bridge"--with a backhanded compliment to Number One. Yet earlier when he received the follow-up distress call from Talos, there was a woman (an uncredited extra actor) at the station receiving it and he didn't bat an eye.
Vena is revealed to be disfigured because the Talosians rebuilt her body without knowing what a human looks like. At the very least, they should have known that human beings symmetrical, as most living creatures are (themselves included), yet Vena is shown with a pronounced hump on her left side and a slouch to the right.