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 Mark Williams shoots the Gill-Man in the water with the harpoon, the creature is clearly facing Mark when shot, and the spear is lodged between the creature's ribcage 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.
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.
After Gill-Man pulls down Chico into the lagoon, when David orders Lucas to tie the bomb, Mark is holding the cigarette high, near his chest. In the next shot, he is holding the cigarette in his left hand which is resting on his leg.
When David and Mark leave the ship for the first time in a little boat to disperse rotenona in the lagoon, Kay stays on the ship desk smoking, with her right elbow leaning on her left folded arm. Between shots, from the boat point of view, she appears with both hands on the lateral rope.
Although the whole story is set in Brazil, in one of the first scenes we see a large sign in the coast reading in Spanish "Instituto de Investigaciones Biológicas", while in Brazil the official language is Portuguese.
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.
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.
When the Gill-Man has the lantern smashed over his head and is set on fire, the fire can be seen stretching out sideways, away from his head on a level plane. A moment later when he dives into the water, the fire is completely away from his head.