It should have been obvious to all those involved that the flattened corpse of Andre would have had a fly's head and a fly's claw on the end of its arm. It is also impossible to believe that both those who removed the corpse from the hydraulic press and the coroner's autopsy of it would not have revealed the truth.
When Philippe shows Francois the spider's web where the fly with Andre's head and arm is trapped, he clearly points to a small white object on one side of the web, which is supposed to represent the fly, while on the opposite side of the web is a large, brown toy spider. In the very next shot - a reverse angle close-up - the hand puppet spider is almost literally on top of the fly.
Francois and the Inspector are the only ones to hear Andre's desperate screams from the web, yet when Philippe pointed out to Francois the fly in the web but didn't hear his father.
At the beginning of the film, in the factory when the night watchman hears the hydraulic press first turn on, the amount of time before he investigates is much shorter that when the flashback is recounted by Helene, plus her screams are not heard at the beginning.
Just before they go to the ballet to celebrate, Andre and Helene share a kiss near the telephone in their home. At the beginning of the kiss, both of them have their heads tilted to the right. When the camera zooms in, they are suddenly tilting their heads to the left.
A fly's vision is not composed of several identical small images grouped together, as is seen in the film.
The lock on the outer door of Andre's lab is installed so it can be opened, without a key, from the outside.
Helene and Philippe try to catch the fly with Andre's head and arm by spreading sugar on the table and the fly goes straight for it. Flies are not attracted to refined crystalline sugar. That has no evolutionary connection.
When Andre explains to Helene how the teleportation process works, he claims that the disintegrated object's atoms travel at the speed of light. Atoms have mass and therefore they cannot travel at light speed; only photons, which have no mass, can do so.
Apparently Andre did not receive the proportional amount of strength a fly would give him, because he had the human amount of difficulty picking up Helene when she fainted.
There is obvious dubbing during the garden scene in the film, which had to be done because the birds in it were singing too loud. In its DVD release's audio commentary, David Hedison admitted to disliking dubbing as an actor and rushing through the scene just so he could get to a flight on time.
The disintegrator integrator only is seen in operation 6x - the ashtray, the newspaper, Dandelo (poor cat!), the guinea pig, champagne, and Andre when Helene begs him to try. Never seen is the fatal mistake with the fly and Andrea getting mixed up.
When the fly with Andre's head and arm is first revealed to have been caught in the spider's web and his brother Francois is completely unaware of it, the fly is struggling in the web. The string used to make the fly shake is clearly visible.
At 1:06:37 into the film, you can see the string that the fly was attached to as it escapes the butterfly net.
When Helene is chasing the fly with Andre's head and arm in the garden and as she stops at the bench, the shadow of the camera is seen briefly on the tree next to her.
When Helene goes to see Andre as he lays on the chaise lounge, they talk about how happy they are that spring has come. The background is full, lush green foliage, which definitely would not happen anywhere near Montreal, Quebec, Canada.
If the teleporter simply, and innocently, switched atoms from Andre's head and arm and the fly's head and leg, how were Andre's head and arm reduced to insect-sized proportions and the fly's head and leg enlarged to human-sized proportions? That would have involved either multiplying or destroying cells on a massive scale in both cases.
When Andre teleports the cat and it does not make it to the other side, the cat is heard meowing. However, the cat couldn't make a sound if it were disintegrated into atoms; it would not have a mouth or a larynx.
After Inspector Charas destroys the spider's web with a rock and crushes both it and the fly with Andre's head and arm to death, the physical evidence of the fly would still have existed, even if in a distorted state. Thus, it was completely inconsistent for him to then continue questioning whether the story of the fly would even be believed, since physical proof of it still existed and would confirm the allegation.
Although Inspector Charas destroys the spider's web with a rock and crushes both it and the fly with Andre's head and arm to death, he actually should have just chased the spider away, allowing the evidence of the fly's existence to be preserved. It seems completely inconsistent that an experienced law enforcement official such as himself would have allowed his emotions (and even his horror at what he had just seen) to overcome him entirely and lead him to abandon his responsibility to save and not destroy evidence, particularly evidence in a murder case.
For Andre to type so fluently, and without any mistakes, with both a dark cloth over his head and his newly-acquired fly vision and arm is highly improbable.