When the giant alligator grabs Henry Silva, his body is horizontal, with the jaws on his midsection and his body hanging out of the sides of the jaws. A moment later, he is spun around lengthwise and sliding down the monster's throat feet first. The giant alligator would have needed to spit the body out and then begin devouring it feet first for that to happen.
When David Madison enters the manhole cover at the end of the film, he is wearing Adidas trainers; when he lands in the sewer he is wearing boots; when he re-appears from the manhole he is wearing trainers again.
The Cadillac limousine switches from a 1971 Fleetwood 75 limousine to a 1966 Fleetwood 75 sedan when the giant alligator crushes it.
When Henry Silva and the gang member head into the alley, they see the shadow of the giant alligator against a wall as it backs down into another alley. A moment later, when Silva investigates, the giant alligator bursts forth from under a mountain of trash bags. No explanation is given for how the giant alligator, after backing down into the alley, covered itself with a mountain of garbage bags.
When the giant alligator attacks Slade's limousine and the camera is on Slade, the car is continually rocking as if being hit. When the scene shifts to the limousine driver, the car is still.
An alligator cannot survive in Chicago. The climate is too cool. This is why alligators are not found north of North Carolina.
The film is set in Chicago, but several scenes in it prove that it was not: during the initial search of the lake, there are palm trees visible in the background and when the search of the sewers is assembling, David Madison is looking at a map of Los Angeles.
In the prologue the family that buys the alligator is shown driving home to Missouri. When they enter Missouri indicated by the "Welcome to Missouri" sign it is clearly California.
At about 30:00 into the film, the reptile expert claims that she "has some non-poisonous snakes at home." Snakes are venomous, not poisonous. (Correction) This is technically not a goof, since the snakes are indeed non-poisonous. And if it were a goof, it would be character error not factual mistake.
At about 30:00 into the film, David Madison and the Chief are driving in a car. Outside the passenger window, a house fly can be seen crawling around the frame between the window and the door, proving that the car is not really moving and that the background passing by is phony.
Sue Lyon is incorrectly credited as an "ABC Newswoman" when, in fact, her character appears to be working for NBC. The microphone she uses during an interview is clearly marked with NBC's initials and the NBC Peacock logo.
The same license plate appears on two very different vehicles (Callan's cargo van and Slade's limousine).
In the first shot of the giant alligator's eye, the entire film crew is reflected in it.
At the wedding, when Slade and the Mayor run to the limousine to get away from the giant alligator, the driver is standing by the door as if everything is normal, despite the panic of everyone else as the giant alligator is going on a rampage.
When David Madison and Marisa are eating at the diner, David tells Marisa he studied psychology before joining the police force. Seconds later, Marisa tells him that Sigmund Freud "said the police want to punish society for their own illicit desires." David then refers to Freud as "this guy," as if he had never heard of Freud, despite supposedly studying psychology.