In outdoor scenes that take place near the door of the Keeper's spaceship (Will and Penny entering and exiting, and their later slingshot-enabled rescue), there are several large boulders. However, none of these objects are visible in the long shot (matte image) of the ship.
We see during the children's dash from the Keeper's spaceship that the control room is just a few feet above ground level (the rise of the outdoor ramp), and that it adjoins a vestibule leading to several long corridors. However, as shown in the long shot of the spacecraft (the matte image), the craft at ground level is a cylinder which is scarcely wide enough for the control room itself.
When the Keeper first speaks to the group of space travelers, he sticks his staff into the ground, leaving it behind as he walks over to the group. After Will notes flowers have suddenly materialized around the staff, the Keeper says "That's the second time today I forgot to turn it off" and he turns around to begin walking back to it. As he turns, however, it is apparent that he is actually carrying the staff at that moment (its bulb head can be seen at the bottom of the screen).
When the Keeper first appears to the group of space travelers and walks up to them, he asks Will "[is there] Something wrong?" At that time Will is leaning over the cage, his forearms resting upon it. Then the image transitions to a two-shot close-up of Will and Penny, and Will is suddenly standing upright.
After the Keeper has introduced himself to the group of space travelers and complained about their having allowed the lizard to escape its cage, he raises his staff into the air to bring the lizard back. When the view then changes from him alone to a group shot, the location of his grip on the staff is noticeably lower.
The Keeper says he collects two animals of every kind, yet when the carnivorous monsters leave the ship there are only four kinds seen leaving (with a fifth - a long-nosed bat - winding up outside the ship at the end). Footage of the monsters is shot over and over from different perspectives and with a hand-held camera, but when doing a body count, we see: 2 black-eyed mummy monsters in black turtle necks, 5 woolly monsters, 6 cyclops monsters (previous seen as the giant in There Were Giants in the Earth (1965)) and 7 cabbage monsters (previous seen in The Raft (1965)).
As the Keeper pursues the children fleeing from his spaceship, he slows his pace to avoid catching up to them so Will has time to activate the door.
Although the Keeper's ship is shown to be wheel shaped, the interior shots of the corridors show them to be straight.
When Dr. Smith and the Robot have entered the Keeper's ship, stunt man Bob May's feet can be heard shuffling across the floor (as he is wearing "the Bermuda shorts") as he approaches the control cluster and again when they exit.
As Smith says "Never mind your twisted sense of humor, release me at once," Don is reflected on the door of Smith's cage. The laughing Don was undoubtedly intended to be visible in the shot, but one can also make out the crew member standing behind him.
After unsuccessfully urging The Keeper to take him back to Earth, Dr. Smith says "Well, let me know if you do [change your mind]." After the word "Well," noise on the set (clacking) can clearly be heard.
The effects of the Keeper's staff on Doctor Smith and the children are puzzlingly inconsistent. It calls Doctor Smith to a cage while having no effect on Will (or, presumably, Penny). While the children are being shown animals inside the Keeper's ship, behaving in a completely normal manner, Smith is zombified the entire time, doing the long walk from the pipe-laying site to the Keeper's ship. Later, when the Keeper uses the staff (while standing just outside of his spaceship) to get the children to sneak out of the Jupiter 2 and walk all the way to him, Smith is unaffected after removing his earplugs inside the Jupiter 2, and remains unaffected during almost the entire walk (the walk which culminates in the slingshot rescue scene).
When asked how the cage can attract an animal, the Robot says, "There is a sonar receiver attuned for high frequency electrical impulses." A receiver could only receive the broadcast signal, it wouldn't be able to produce it.
After John frees him from the cage, Smith makes no mention of having seen the Keeper. However, Smith had been watching the gorilla-like beast in its cage as it disappeared, leaving him with a direct line of sight to the Keeper.
Despite the one in The Derelict (1965) having been far larger, Will exclaims (upon seeing the Keeper's spacecraft) "It's the biggest spaceship I've ever seen!"