The Man in Black's dislocated right shoulder miraculously healed itself. During the party, he was unable to even lift his arm to light his cigarette but by morning it was healed and strong enough to be able to leverage himself off the ground. No evidence of this injury was ever seen again.
Early in the episode, Antoine Costa examines the skull of the dead native American. There is no gunshot wound to his face and no blood is visible. Right afterward on the flashback scene, Dolores shoots the native American in the face.
When Bernard and Charlotte are in the underground facility, the outlines of Tessa Thompson's wireless microphone pack is clearly visible strapped to her upper right leg.