Enforced Method Acting: Quite a few of Nathan Fillion's stunts involved a self-inflicted version. In his final fight scene against the Operative, he ended up slamming his face into the floor a few times; Joss was simultaneously impressed and horrified, and it took the makeup crew a moment to work out that he'd not only swollen his face, but also that he was somewhat dazed and struggling to read stuff in the background.
Early storyboard sketches (some can be found in the Serenity companion book that has the shooting script) seem to show that River was going to be barefoot the entire movie. For example, she's seen barefoot in the storyboard for River's fight with the Reavers.. The novelization also seems to go along with this idea that River is barefoot throughout, as the narration mentions her being barefoot in the scene where they discover the dying Shepherd Book, even though she actually has boots on in that scene in the film.