- Continuity: When the Operative is reviewing Mal's file, Mal's first name is spelled "Malcom", then "Malcolm".
- Continuity: 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.
- Continuity: Security camera footage shows Mal and Jayne sitting at a table with Fanty and Mingo before they enter the bar.
- Continuity: 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.
- Continuity: 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.
- Continuity: 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.
- Continuity: 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.
- Revealing mistakes: Kaylee finds a dead boy. If you look near the gunshot wound in his stomach, he is still breathing.
- Revealing mistakes: 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.
- Crew or equipment visible: When Jayne comes running down the stairs to tell Mal that Reavers are in town, you can see the set on the left of the shot.
- Revealing mistakes: 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.
- Continuity: 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.
- Continuity: 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.
- Revealing mistakes: After River kills all the Reavers, he blasts through the wall. A "dead" Reaver at the bottom left corner of the screen flinches.
- 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.
- Incorrectly regarded as goofs: 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.
- Incorrectly regarded as goofs: 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.
- Revealing mistakes: 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.
- Continuity: Simon is shown personally rescuing River in the movie, but during the series pilot episode, Simon tells how he paid others to rescue her.
- Plot holes: Mal says Simon has River on his boat 8 months. But this movie takes place six months after the show's end, plus original series time, that means she's been on the ship closer to 18 months.
- Continuity: 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.
>>> WARNING: Here Be Spoilers <<<
Goofs below here contain information that may give away important plot points. You may not want to read any further if you've not already seen this title.
- Continuity: 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.
- 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.
- Revealing mistakes: SPOILER: On Miranda, when Simon comforts River as she says "Please God make me a stone. . ." his eyes follow the camera rotating around them. He looks directly at it for a split second before it pans up to Jayne.
- Continuity: 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.
- Continuity: 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.
- Continuity: SPOILER: After leaving the planet Miranda, and leading the Reaver ships into the Alliance ships, when they attempt to land they only have 20% engine power, and the pilot says he will "glide it in," we see the ship crashing through a hanger and during this time we see the left engine get sheared off by a pole, and not seconds later, we see the same left engine (magically back attached to the ship where it was) get sheared off again by a different pole, with the right engine already missing (film was flipped) and then, after the ship spins 180 degrees, we see a back shot of it falling into a pit, with the right engine intact and the left gone, and then it cuts to a front shot of the ship in the pit, with the right engine intact and the left gone.
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