Movie Goof (continuity error): At the end, when Serenity is about to take off, it is raining. Yet,in the conversation between Mal and the operative during this time, we can see that they are both dry as a bone.
Movie Goof (revealing mistake): When River somersaults through the hatch, just after Simon is wounded, she is wearing a brace on her right knee. The brace disappears in the next shot.
Movie Goof (incorrectly regarded as a mistake): On Mr. Universe's planet the audience is told Kaylee rigged the blast doors so no one could open them once they are sealed. Yet, right after Mal asks about River, the blast doors do open. The doors were obviously malfunctioning earlier when they only closed halfway.
Movie Goof (continuity error): The wide angle shot of the security camera footage, when Mal and Jayne first enter the bar, shows a time stamp that doesn't change when the camera zooms in.
Movie Goof (continuity error): Security camera footage shows Mal and Jayne sitting at a table with Fanty and Mingo before they enter the bar.
Movie Goof (revealing mistake): When the operative and Mal are fighting in the temple, the operative kicks his gun from his hand. The operative is clearly a stunt double.
Movie Goof (continuity error): When the operative says, "Stop Backtrack, stop!" River looks straight ahead. When the Operative emerges from the record projector, River is looking to her left.
Movie Goof (revealing mistake): Kaylee finds a dead boy. If you look near the gunshot wound in his stomach, he is still breathing.
Movie Goof (revealing mistake): When the Serenity is hit by the Reaver's EMP and begins to crash onto Mr. Universe's planet, Wash strains against the force of rotation while he reaches for a panel of buttons on his console. Not only does he change where he is reaching for, when his hand hits the panel the entire panel moves: it was made of cardboard.
Movie Goof (continuity error): When the Operative is reviewing Mal's file, it lists his service rank as Captain, whereas in the series he was only a Sergeant by the battle of Serenity Valley (where the Independents surrendered, and his military career ended). His civilian rank is Captain.
Movie Goof (continuity error): When the Operative is reviewing Mal's file, Mal's first name is spelled "Malcom", then "Malcolm".
Movie Goof (continuity error): When Mal and Zoe talk about the man left behind during the bank job, there's an orange/yellow light flashing that reflects off of the right of Mal's face but not at all off Zoe's, even though they're standing right opposite each other.
Movie Goof (factual errors): The Chinese writing throughout the movie is nonsense. For example, a pod marked "Search and Rescue" in English says "Hillock thus for it minor" in Chinese.
Movie Goof (continuity error): When Simon rescues River at the start of the film, he smudges the spot of blood on her forehead. When they leave the room the spot is no longer smeared.
Movie Goof (revealing mistake): After River kills all the Reavers, she blasts through the wall. A "dead" Reaver at the bottom left corner of the screen flinches.
Movie Goof (continuity error): At the start of Dr. Caron's holographic recording, there is a noticeable delay before she says, "... .and you can see, it isn't what we thought". When the recording is replayed and broadcast at the end, the delay is gone.
Movie Goof (incorrectly regarded as a mistake): On Miranda, around the time of River's "Make me a stone" speech, Jayne turns around to the left. In the next shot, he turns around to the right. In the commentary for the special edition, he admits that he did it on purpose.
Movie Goof (continuity error): When Jayne passes the jug of Blue Sun to Simon, the label is facing Jayne. When Simon picks it up to drink, the label is facing Simon.
Movie Goof (continuity error): In the very last scene, when River and the Captain are flying the ship, Mal presses a button, which lights up. In the next shot the light is off. In the next shot, it is on again.
Movie Goof (continuity error): SPOILER: When the dying Shepherd Book removes his blood-covered hand from Mal's face, it leaves no blood on Mal's cheek. Subsequent shots show smudged blood.
Movie Goof (continuity error): SPOILER: In the big gun battle between the crew and the Reavers, just as Zoe fires her shotgun for the first time, Inara is in the background, holding a bow and arrow instead of the bolt thrower she is supposed to be using. The bow-and-arrow was the original weapon used, but it was replaced in post-production due to test audience reactions.
Movie Goof (crew or equipment visible): SPOILER: When the operative tells the Alliance soldiers to stand down, one soldier (almost out of frame) lowers a set microphone.
Movie Goof (continuity error): SPOILER: While being chased out of town by reavers, the mule wipes out a market stall and its yellow awning. As the reavers then pass the same spot, the awning and market stall are still intact and in place.