Continuity mistake: After getting Spock and Bones beamed up and out of danger, Kirk is running away from "God." As he pauses outside of the shuttle craft, you can see the dark spot where he got zapped is gone.
Visible crew/equipment: During the fight sequence between Kirk and Spock's brother Sybok you can see crew's hands helping lift Kirk up when he is being thrown. (Far right of screen).
Revealing mistake: On Sha-Ka-Ri, after Kirk says "I seek proof", and the camera goes to "God", then back, you can plainly tell it's a stunt double, and see the wire connected to the harness he's wearing to pull him backwards after getting zapped.
Continuity mistake: After Kirk throws the Cat woman dancer, he drops his arms. A second later, they are up again.
Factual error: When Kirk falls off El Capitan, he is shown falling all the way past the tops of the trees. I have been to Yosemite and the trees are tall, but not tall enough to give Spock enough time to slow then stop Kirk's fall.
By the time Kirk reaches the top of the trees, he is traveling at terminal velocity (assuming Kirk was halfway up, about 2000 feet from the ground, and an initial fall rate of 32 feet per second, per second), approximately 120 mph, about 200 feet per second. If the trees were 1000 feet tall and Spock caught Kirk right at the top of the trees, that would give him 5 seconds to slow down and stop Kirk. Impossible. Fortunately, in the movie he was able to accomplish this feat, or it would have been a very short movie. :).
Visible crew/equipment: When the being they think is "god" shoots Kirk with lighting eyes, you can see the pull wire on his back as he flies back.
Continuity mistake: At the camp fire the whiskey bottle never empties. Almost empty, then full again.
Other mistake: If Uhura was supposed to recall the rest of the officers over a priority seven situation why did it take so long to go get Kirk, Spock, and McCoy?
Continuity mistake: As Sybok mentions Sha-ka-ree, his head tilted to his right. On the monitor outside the brig, it's tilted left.
Other mistake: In the fight in Paradise City, the Enterprise people have shields that they didn't have in evidence when they ran out of the shuttle.
Continuity mistake: As the shuttle nears the ship, they stop and are looking at the port side of the Enterprise. Inside the shuttle, as Talbot turns from looking out, the shuttle is pointed directly at the aft section, towards the shuttle bay. The it's back to port to begin the risky maneuver.
Other mistake: As the shuttle craft approaches the planet, there is only a view of the stars, rather than any of the mountains or other scenery.
Continuity mistake: In the opening scene, it is seen that Nimbus III is an arid place, but at one point when Sybok goes to get his horse, there is a flash of blue sky with white clouds. In rest of the scene it's yellow and dust filled.
Continuity mistake: As the shuttle with Kirk and company nears the shuttle bay, the guide strip lights pulse in a slow, staggered fashion toward the wall. After the angle change, the lights pulse in a faster, smoother succession.
Continuity mistake: After the Bird of Prey blasts "God", it turns to Kirk. After he says "What are you waiting for?" he gets beamed up. He has his arms up in a defiant manner. When he materializes on the platform his arms are mostly by his sides.
Audio problem: When the Enterprise fire the torpedo, the sound used is the old series sound used when the ship's phasers were fired, not the correct noise for a torpedo firing.
