The Gill-Man breaks loose of his chains, leaving the leg iron on his left ankle. The shackle remains on him in every dry land scene (where the Creature is played by Tom Hennesy) but in all the succeeding underwater scenes (where he's played by Ricou Browning) the leg iron is missing.
When the Creature goes into the Lobster House restaurant looking for Helen, there is a clock on the wall over his head. When he leaves moments later carrying her, the clock has moved forward more than 2 hours.
When the man's dead body is found on the beach he is lying in a different position than when he was attacked and killed.
While Joe is walking the Creature through the pool, shots change and the Creature is suddenly a foot deeper than before.
The scientist puts the Gill-Man into a saltwater tank filled with sharks, sea turtles etc. The Gill-man came from a freshwater lagoon in the Amazon.
Flippy the "Educated Porpoise" is not a porpoise but a dolphin.
When Professor Ferguson is informed of the capture of the creature, his colleague refers to it as a "creature from the Devonian era" and something that should have "...died out a quarter of a million years ago."
The Devonian is a geologic period, not an era (which marked the emergence and divergence of fish species and land plants, and, near its end, the first animals to venture onto land), and lasted from 416 million years ago to the beginning of the Carboniferous Period, 359 million years ago. As with the first Creature movie, the "scientists" not only do not know the terminology of geologic history, but their chronology is all wrong.
One of Prof. Ferguson's displays is a demonstration of how a well-fed cat won't kill mice. This is true of many predators, but cats (sometimes) kill things for fun.
When they use dynamite to stun the creature before capturing it, the creature floats to the surface, however when they drug it with a doctored fish it lies at the bottom of the tank. There doesn't seem to be any good reason for the difference.
At 1:10 the police boat is traveling at a high rate of speed, yet the officers clothes or hats do not even move from the wind, suggesting that they were in front of a rear projection screen.
Each time the Creature swims up to the window in the tank to see Helen, you can clearly see air leaking out of the top of the Creature's head, not from his gills or mouth.
At around 1:12 when the two young gentlemen find Helen washed ashore the passenger grabs a flashlight to illuminate her body, but the light does not match his movements.
When the gill man is underwater , you can see the air bubbles not only coming out of the top of the costumes head , but also from the one of the eye sockets .
Early in the movie, when the men on the RITA II are shooting at the Creature, one of the projectiles meant to simulate bullets streaking through the water can clearly be seen bouncing off the Creature's back.
George calls Lucas "Lucas" but Lucas calls George "Joseph" (the name of a third character standing next to George).
In the scene where the Creature attacks a pair of college students, it picks one of them up and tosses him into a nearby palm tree. The line attached to the stunt double is clearly visible as he hurtles through the air.
During the film's opening scenes on the Amazon River, the distinctive call of the Laughing Kookaburra from Australia can be heard; however, this bird cannot be found in South America.
When the Creature drags Joe over the side of the holding tank into the water, two men jump in to save him. The Creature drags both of them under the water. When Joe jumps back in to save them, he only drags one to safety, apparently leaving the other one to drown.
During the performance of Flippy, the educated dolphin, the announcer introduces the final trick of raising the flag. After doing that "final trick" Flippy does several more tricks.