In the film, when Francois and Philippe visit Andre's laboratory from the previous film The Fly (1958), the messages Andre wrote to Helene on the blackboard can still be seen on it. But at the end of that same film, Helene had told Inspector Charas that she had erased them all off of the blackboard in order to cover up all traces of Andre's experiment.
At the beginning of this film, Francois and Philippe go to Andre's laboratory at the foundry, but in the previous film The Fly (1958), the laboratory was in the basement of the Delambres' house.
At around 23:00 into the film, Max Barthold is eating and keeps alternating between holding a fork and a glass of wine, then back to a fork.
In the film, when the Fly comes out of the teleporter cabinet, he breaks the glass walls; however, at the end of it he is put back into the cabinet and the glass walls are somehow fixed.
In the film, although Philippe receives not only a fly's head in the transformation, but also a fly's claw replacing both his left hand and his right foot, the fly only receives Philippe's head and still has all six of its legs, apparently both intact and functional.
In the film, after Philippe has undergone the transformation and is running through the forest while being chased by the police, he hits his head on the branch of a tree and immediately adjusts the headpiece with his hand.
In the film, when Alan/Ronald is about to run the detective's car into the lake, he first takes a rock and places it on the gas pedal of the car. During that same scene, when he is leaning into the driver's side of the car, an arm reaches up for the steering wheel - obviously the arm of the stunt driver who was going to drive the "driverless" car.
The film is set in Montreal, Quebec, Canada, yet all the public signage is in English. Provincial law in Quebec requires that all signs must be in French, which must be more prominent than any other lettering (usually English) on the same sign.
Philippe was a child in the previous film The Fly (1958) and in this film, he is an adult. Vincent Price plays Philippe's uncle, Francois Delambre, in both films, yet in this film he looks the same as he did in the previous film when he should have looked over 20 years older. As Philippe was about 10 years old in the previous film, this might only be over 10 years later, and Price was given gray hair at the temples which is, however, not very clearly shown in this black and white film.
In the film, the fly-headed, -armed and -legged Philippe, during his search for Alan/Ronald, turns up at the morgue and kills Max Barthold. Why and how would he do all of this? Philippe knew nothing of Max Barthold, his connection to Alan/Ronald, or of the morgue before all of this happened.
Inspector Beauchamp's name in the film is pronounced by many of the characters as "Bee-champ". Any French-Canadian worth his salt would have pronounced it correctly as "Bo-shamp."
One character in the film mentions creating radar for the Canadian Air Force. Since 1924, it has actually always been known as the Royal Canadian Air Force.