In one shot, the Ariel crew have their insignia on the wrong side of their uniforms.
Lt. Cmdr. Markel has Commander stripes.
In one shot Spock has normal human eyebrows.
The Ariel crew appear to wear the same insignia as the Enterprise. During the original five-year mission, different starships had different insignia.
Trivia: This episode features the only time in the series that anyone dies on-screen.
When the Slaver weapon is in "power drain" mode, why does it not drain the life support belts? It drains the police net.
When Spock first sees the miniaturized AI computer, he expresses astonishment that it's so small. But a minute or two later he says that the matter-conversion weapon is the only item the Federation doesn't already have. So which is it?
When Chuft Captain initially tests the slaver weapon, the weapon changes differ between what he holds and what he points at Sulu. At several points it reverts backwards, changing repeatedly and out of sequence from communications device to laser to telescope and back again.
Spock's life-support belt disappears in one shot.
When the trio exit the shuttlecraft through the rear exit, the doors slide into the sides...except the sides are minimally thin. There's nowhere for them to go.
The aquashuttle lands during the day. However, when Kirk calls Scotty for beam up, the sky behind him is a night sky.
When Kirk and Spock begin to explore the ruins of the old city, one shot shows Spock's uniform colored gold instead of blue.
For some reason when Scotty is on the bridge briefing Kirk and Spock on the engines, nobody else is on the bridge. Given they're in a potentially hostile situation with time running out for them to analyze the situation and respond to it, why would the entire bridge crew leave, regardless of the shift.
Trivia: The Elysian Council appears to be made up of; Xerius (a Romulan), Devna (an Orion), a Klingon, a Kzinti-like creature but somewhat chubbier (see "Slaver Weapon"), an Andorian, an antlike creature, a plant creature (similar to the Phylosians in "The Infinite Vulcan"), an Aquan (perhaps from the planet in "The Ambergris Element"), a Vulcan, a Tellarite, a Human in an old-style Federation uniform, and a Gorn.
Kirk refers to the stardate as "52.2". Later he refers to it (correctly) as "5267.2" - they left out the "67" in the earlier reference.
After becoming smaller, Lieutenant Arex mentions that his eyes no longer reach his station's opticals, but the navigator station has no opticals.
If the space between the atoms is reduced but the weight of the shrunken objects remain the same, the crew would soon find it hard to move under their own weight. To say nothing of what would happen to the ship to beam aboard an entire city of perhaps diminutive size but gargantuan weight.
The crew somewhat confusingly alternates between using metric measurements ("1 centimeter high") and imperial ("we are going down to 1/16th of an inch high").
Spock notes that the coral in the aquarium is shrinking along with them. However, as he states that, the shot shows the coral coming up to his neck. The aquarium was not large enough to hold coral that big in previous shots.
When Chapel recovers the miniature laser, it is a solid disk. It is still a solid disk when she walks along the shelf and trips. However, when she falls into the aquarium, it is a torus. When she gets out of the aquarium, it is solid but with an inscribed circular line in the center.