According to Nathan Fillion, he personally supplied the blueprints used to build the ship set in the film after being informed at a production meeting that the originals had been lost. He was able to do so because, being so excited about being in the original show, he had taken photos of ALL the preproduction materials he had seen, including the blueprints.

In his DVD commentary, Joss Whedon said Chiwetel Ejiofor, Nathan Fillion, Summer Glau, and Sean Maher performed many of their own stunts. Glau, a trained dancer, used her dancing skills in River's two fights. For the second fight, the cameraman, who was also a dancer, moved through a gap around the combatants to achieve the movie's dynamic camera angles.

In the cargo bay, just after a Reaver is shot, some of the crates behind River have the message "Reusable Container: Do Not Destroy" printed on them. It's an inside joke. The ship set had to be rebuilt from scratch for the movie because the original, from Firefly (2002), was destroyed.

According to the director commentary, Mal's line, "Faster would be better," was ad-libbed by Nathan Fillion when Joss Whedon told him to "say something Mal would say."

The cast had a running gag where they would yell Summer Glau's name whenever any of them flubbed a line or forgot to do something. It originated on Firefly (2002) when she forgot her line at the end of a very long and difficult scene. (Nathan Fillion, Morena Baccarin, and Sean Maher can be seen doing this on the DVD blooper reel.)

Continuity

Security camera footage shows Mal and Jayne sitting at a table with Fanty and Mingo before they enter the bar.

When Simon is rescuing River, the Alliance doctor tells Simon about the Alliance's intentions with her and the other subjects of their tests, including the goal of turning them into weapons. In the original television series however, Simon does not know anything about these procedures. This was included so that the film would make sense to viewers that had not followed the Firefly (2002).

When The Operative examines the footage of River's bar fight he brings up information on Mal. It describes him as a captain in the independence army. All through the series he was said to be a sergeant. Captain was the title given to a commander of a star-ship. It was also a military rank. Malcolm Reynolds is captain of the Firefly Class transport Serenity. He got promoted to military Captain due to his heroics at the Serenity Valley battle.

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.

After they do the 'Barn Swallow' technique after being chased by the Reavers in the beginning, Jayne is in the Mule. When Kaylee comes down the stairs, Jayne is also on the stairs. After Simon hits Mal, it goes back to Jayne pouring alcohol on his wound, and he is back in the Mule.



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.

On Mr. Universe's planet Kaylee says she COULD rig the blast doors so no one could open them once they are sealed. She was injured in the fight, so never managed to do it, which is why right after Mal asks about River, the blast doors do open. The doors were obviously malfunctioning earlier when they only closed halfway.

When the Operative is knocked out by Inara's incense-flashbang, Mal could have easily taken another second to shoot him in his head before fleeing the scene. However, murder of this sort is completely against Malcom's character.

When Mal and Zoe talk about the man left behind during the bank job, an orange flashing light reflects off Mal's face, but not off Zoe's, even though they're standing opposite each other. This light is fire from the bridge windows as Serenity leaves the planet. This is explained in the commentary.



Revealing mistakes

When Serenity is hit by the Reavers' 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. When his hand hits the panel, the entire panel moves; it was made of cardboard.



Crew or equipment visible

In the wide shot of the bar scene that Mr. Universe is watching, the camera operator is visible, in an orange tee shirt, in the upper left hand corner of the shot just before he says the line, "And she falls asleep."



Character error

When The Operative is reviewing Mal's file, Mal's first name is spelled "Malcom", then "Malcolm".

When Simon is with River in the storeroom he asks her if she remembers saying anything when was triggered and states the captain heard her say something on the security feed. However the first time Mal sees the feed is while the crew is talking to Mr. Universe which is taking place at the same time Simon is with River meaning he wouldn't be aware of anything that was heard on the feed.

In a conversation where Mal talk about the itinerant nature of their existence, he says "When the wind blows northerly, I go north", indicating he goes whichever way the wind blows. But a northerly wind is a wind that blows FROM the north, so a sailed vessel would tend to go south on a northerly wind.