The overhead Enterprise bridge shot at 8:03 (used often in this animated series) shows Spock at his bridge station when he's also down on the planet, abducted by the Phylosians. He is left of Uhura in the overhead shot, in his blue shirt, but when the perspective changes to floor level, the figure at Spock's station - whoever he is - wears a red shirt. Later at 8:40, as Sulu says "Aye, sir," blue-shirted Spock appears at his station once again. (Another overhead bridge shot appears at 17:51, but it's adjusted for absent crewmen - unless that's supposed to be Sulu at the helm when he's also on the planet with Kirk and McCoy.)
Kirk's second landing party finds Spock lying on a machine. Kirk removes him from the machine and Dr. McCoy monitors him as he lies on the floor. When Stavos smashes the machine, Spock lies on it again. The next time Spock is shown, he's back on the floor.
In the final third of the story, Kirk (with McCoy, Sulu and Spock either by, behind or around him) faces gigantic Spock 2 and Stavos Keniclius 5. Scenes continuously flip between showing Kirk alone or showing him with his men. And at one point (at 19:57), Kirk and McCoy are shown standing between the giant feet of Spock 2.
McCoy mentions his grandfather's weed spray "brewing in sickbay." This would not be necessary. He could have given the formula to the ship's replicators and had it produced instantly; however, McCoy is a bit obsessive and quirky about certain high-tech matters (e.g., his legendary discomfort with transporters in Star Trek (1966)), so he might regard a replicated weed spray as inauthentic.
At approximately 20:18, the close-up of Sulu's head as he declares "The Vulcan Mind Touch" shows his neck stopping at the collar line. In other words, his body is missing.
When Kirk orders Sulu to "stay here" at 2:19, there are four dirt smudges on Sulu's neck and face that disappear when he moves. The first gel was obviously not clean.
In the transporter scene, Scott's last line is given an "intercom" effect, although he's in the room.
The Phylosians are absolutely identical, yet Kirk grabs one from behind, calls it by name ("Agmar") and is correct.
Spock 2 - a giant like Stavos Keniclius 5 - is introduced wearing his Starfleet Federation uniform. Though Spock himself has been cloned and gigantified, his clothes could not have been. They would have to be manufactured - including his giant comm badge and his boots - and there would be no need to go to all this trouble. (And where would one get boot leather on an all-plant planet?)
Of the little purple mobile plants (called retlaws), Sulu says they're all over the place, yet only one is ever seen. (Multiple little tufts are seen in only one shot at 3:28, but these are green rather than purple.)
Sulu calls the Vulcan Mind Meld the Vulcan Mind Touch.
At several points, both Kirk and Bones refer to Keniclius as Kaniculus.