Papillon walks through the abandoned Indian village, looking for its inhabitants, and finds a small packet hanging from one of the huts. The packet contains seven pearls. (He probably pays one pearl to the bus driver for the trip to the border, but that is unknown.) He gives one pearl to the Sister for the wagon-ride to her convent, and that pearl appears on the Mother Superior's desk. That would leave no more than five or six pearls remaining in his possession, but he empties his packet and hands all seven pearls to the Mother Superior to give him sanctuary.
When the random prisoner has his head cut off, if you watch it slowly, you can see the blade come down and stop, then the next cut (at the same angle) has a dummy's head rolling. Additionally, in the latter cut the Sun's position has changed, so it is now in the frame.
(at around 1h 20 mins) The shaving cream pattern changes.
When the guards start to open the alligator's belly and shout "Move it! What the hell you looking at!" Dega is wearing his long-sleeve dirty gray shirt with a wide brim hat (with nothing in his hands, i.e. his striped shirt), and Henri is wearing a headband across his forehead. Moments later, when they walk towards a log to sit down, Dega is now wearing his orange and white striped shirt with a bandana type headpiece and Henri's headband is now wrapped and tied around his neck.
(at around 35 mins) The prisoner's uniforms are cleaner than they were just prior.
When Papillon is in his first solitary confinement, a vampire bat bites him and drinks his blood. The wound is two fang-like holes where the blood comes out. A vampire bat doesn't have fangs for teeth. Using their sharp teeth, the bats make tiny cuts in the skin. The bats' saliva contains a chemical that keeps the blood from clotting. The bats then lap up the blood that oozes from the wound.
The guillotine permanently erected in the prison courtyard is a piece of pure Hollywood. By the 1870's, the French had developed demountable guillotines that could be easily transported and set up in the town square wherever an execution was to take place, taking only an hour or so to assemble and dis-assemble. There is ample evidence that the 'bagne' (Caribbean penal colony) had one of these, which would have only been brought out of storage when needed. Had it been left permanently exposed to the tropical sun and rain, its timbers would have very rapidly deteriorated and warped to render it unusable.
The alligator the two are supposed to grab has its mouth tied shut.
When Papillon is in the natives' village, he goes swimming with one of the girls who has tan lines from a bra/bikini top.
Newer prints, with improved resolution and brighter tone reveal that the leader of the leper colony's mouth isn't moving at the end of the "cigar" conversation, when he talks to McQueen.
As Dega is boarding the boat to French Guyana, his ear plugs are visible.
Dead Julot's eyelids visibly moving under the pouring rain (in the close up with his neck to the left and forehead to the right of the screen).
When Papillon first visits the lepers, the leper he speaks to does not move his lips (probably because of makeup).
At the end of the film, when Papillon is floating on his bag of coconuts, a scuba diver is clearly visible in the water beneath that bag.
A harness is visible on Papillon's midsection as he helps Dega over the wall.
At around 18:00, you can see the shadow of camera or crew as the rail car passes.
At a scene in St. Laurent, there are mountains in the background, presumably on the Suriname side of the river. There are no mountains in that part of Suriname.
During the sailboat escape, the boat is seen sailing right to left against the setting sun, that is due south, but sailing from the prison in French Guyana would require sailing north and/or west.
It is highly implausible (and never explained) why the escaped trio would need to sail their boat all the way to Honduras, a country in Central America and several thousand miles away from French-Guiana. Why not sail along the coast due south to Brazil or north-west to Venezuela? In fact, in the autobiographic novel on which the movie is loosely based, Papillon (Henri Charriere) eventually escapes to Venezuela.
When they are on the cliff top looking at the waves, Steve McQueen says the mainland is only 24 miles. In fact its just over 8 miles in a straight line.
Camera boom shadow is visible during the rain storm from around 42:00 as each person passes the camera.
Unless he is a complete quack, the doctor does not know that a chest X-ray should be done with the heart closer to the frame (face down) to make sure that the heart silhouette is not artificially enlarged. He specifically asks Papillon to lie down on his back.
Unless he is a complete quack, the doctor does not know that a plain abdominal X-ray should be done with the spine closer to the frame (face up) to make sure that the bony silhouette does not mask some of the bowels by being artificially enlarged. He specifically asks Papillon to turn around and face down.
Unless he is a complete quack, the doctor does not know where to listen to a patient's heart and speaks at the same time, which renders auscultation practically impossible.
Papillon "faints" when going for a 6th step but he had been walking very small steps for weeks or months in his cell due to extreme weakness so the "6th" step should not have resulted in such a psychological issue.