Trivia: Dustin Hoffman wore contact lenses so he could see correctly wearing those thick glasses.
Trivia: In the book the tribal island girl who takes care of Papillon after he escapes is 12 years old. The film's producer made her older for all the obvious reasons.
Trivia: Dalton Trumbo, the film's scriptwriter, has a cameo as a Devil's Island Prison Commandant.
Answer: It does appear to be unintentional (or at least, unscripted), but they continue because when you're shooting a movie, you don't stop until you hear "cut", and especially at that time animal welfare wasn't necessarily a priority. I'm guessing no-one was concerned about the chicken, and so didn't feel the need to do anything about it. It's possible the film was made without an animal welfare monitor on set. As to why it's in the movie, the whole "marching to the prison" sequence was probably handled by the assistant director (as shots like this, not involving the principals or any substantive dialogue, often are) and they may have only done the one take. Who knows, they may have thought the injured chicken added realism to the scene.