The Gill Man destroys the Rita's boats to prevent any escape. Yet, when he kidnaps Kay, David tells Lucas and Prof. Maia to get to the beach entrance of the cave. There are no boats available to go ashore, yet both men arrive to save David and Kay in dry clothes. Indeed, when The Gill Man staggers out of the beach entrance to the water, there is no boat in sight.
When Kay is shown swimming in the river from above, the water has only about 12" of visibility. When the camera films her swimming from underwater, the water is crystal clear with unlimited visibility.
When they follow The Gill Man into the water and then find his tracks in the sand, the tracks are webbed feet, but when he is seen, he has long fins on his feet like divers use.
The wet footprints left on the deck of the Rita don't match the way the Creature walked. He dragged his feet on the ground, but the prints are from something that picked up its feet after each step.
When Mark Williams shoots The Gill Man in the water with the harpoon, the creature is facing Mark when shot, and the spear is lodged between the creature's rib cage and the abdomen. The Gill Man is holding the spear in place in the establishing shot. In the next shot, as The Gill Man swims away, the spear and the wound have moved to the creature's back, as if Mark had shot him from behind. From that angle, The Gill Man can't hold the spear in the same manner.
Doctor Reed describes the lagoon as appearing just as it was "150 million years ago, during the Devonian Age." The doctor's geologic timescale is in error by at least 200 million years. The Devonian period began 417-416 million years ago and ran to 360-354 million years ago.
The scientists in this movie, presumably geologists and palaeontologists, constantly misuse terms for the geologic time scale. They refer to the Devonian as an "age" and as an "era"; both terms are wrong. The Devonian is a period, which is longer than an age and shorter than an era. Geologic time is divided in units termed, from longest to shortest, Eon > Era > Period > Epoch > Age. The current year is part of the Holocene age of the Quaternary epoch of the Cenozoic era of the Phanerozoic eon.
The film is set in Brazil, yet the native captain and guides speak with Spanish accents and use "sí" for yes instead of Portuguese "sim."
While the film is set in the Amazon, calls from Indonesian Siamangs and Ring Tail Lemurs from Madagascar can be heard.
Kay remonstrates with the divers that they didn't wait long enough before surfacing, presumably to avoid nitrogen narcosis (the bends), but they didn't really dive deep enough to make that a major concern.
(at around 1h 14 mins) When the trees barricading the exit of the lagoon are removed with a winch, the bottom end of the tree trunks show that the logs were cut down by a saw.
(at around 50 minutes) Just after the divers enter the creature's grotto, there appear to be two pillars and perhaps part of a structure in the background that are not noticed by the characters. This anomaly may be due to reuse of a backdrop painting, but there is no suggestion that other viewers have noticed it (and that there's no mention in Bill Warren's 'bible' of 1950s Sci-Fi films). If the answer is known, perhaps it could be added to the film's 'Trivia' section.
In one shot where the "Rita" is steaming up-river and into the lagoon, a telephone pole can be seen in the background, just above the treetops.
When Rita is steaming up the Amazon River (as opposed to on the lagoon), the water is generally still, river water which should be moving more than is shown.
When Dr. Thompson is guarding the creature, the lever on his lever action rifle is missing.
When the Creature is deep at the bottom of the lagoon looking up at Kay as she swims, the dark silhouette of a very long and large cable suspended above the water can be seen above her.
Although the whole story is set in Brazil, in one of the first scenes there is a large sign on the coast reading in Spanish "Instituto de Biológia Marítima", while in Brazil the official language is Portuguese.
The tributary is said to "end" in a closed-off lagoon due to a geological event. All tributaries by definition end by emptying into another river.
Among the many jungle birdcalls heard in the Amazon is the cry of the kookaburra, an Australian species.
The whole premise of a geological event happened, which broke off a bunch of limestone, which washed into a lagoon to be found millions of years later is utter nonsense. The geologist in the party especially should have known that limestone dissolves in water, running water breaks down most anything (look at the Grand Canyon) given any amount of geological time.
Archaeologists, paleontologists, and geologists everywhere cringe when Dr. Maia quite literally rips the creature arm from the rock in the first scenes. Even early geology students would know to take more care with such an impressive finding.
Early in the film when the Doctor was photographing the claw fossil, he pulls the slide on the film carrier, he reinserts it the same as he pulled it out. With that type of film carrier, the slide has black on one side and silver on the other. When the film is loaded, the slide is put in with the silver side out. After exposure, the slide is reversed with black side out. This lets him know what side is exposed and which is unexposed.