The film's cast--in particular, Jonathan Frakes, Marina Sirtis and LeVar Burton--have leveled fierce criticism at director Stuart Baird over his direction of the film, claiming the director hated the Star Trek universe and knew nothing about it. Baird, for his part, expresses his frustration in the DVD commentary at having to tell a story in an established universe with pre-existing design and character relationships, hated having to utilize recycled sets and props and has trouble remembering the names of the main cast.
Every previous Star Trek series gets some sort of mention or reference. There's a maneuver named for Captain Kirk from Star Trek (1966). There is mention of the Dominion War from Star Trek: Deep Space Nine (1993). Captain Janeway from Star Trek: Voyager (1995) has a cameo. And one of the ships that the Enterprise was to rendezvous with is the USS Archer, named for the captain in Star Trek: Enterprise (2001).
Midway during shooting, the captain's chair from the bridge set disappeared, apparently stolen. While the film crew scrambled to find a way to work around the problem, the Star Trek: Enterprise (2001) cast and crew shooting in the soundstages next door decided to have a little fun at their franchise-mate's expense: Scott Bakula visited Patrick Stewart's trailer to present him with a makeshift wooden "replacement" chair with the letters K-A-P-T-I-N painted on it.
Aside from the explosions, the ramming of the Scimitar by the Enterprise is not computer-generated. The filming crew actually ran a model of the forward saucer into a buildup of the Scimitar, shot it in slow motion, and hung it upside down to give the illusion of the hull flotsam drifting into space.
Nicholas Meyer was approached to direct the film by Rick Berman, but told Berman that he would want to do a rewrite of the screenplay. Berman was forced to refuse, as he had already promised John Logan full control over the screenplay, and so Meyer respectfully turned the offer down. Berman next considered offering LeVar Burton the chance to direct, but was then ordered by the studio to hire Stuart Baird.
After Star Trek: Generations (1994), Michael Dorn (and thus Worf) joined the cast of Star Trek: Deep Space Nine (1993), and since then his character has been a source of awkwardness. In Star Trek: First Contact (1996), Worf pilots the Defiant, he is beamed aboard the Enterprise-E after the Defiant is no longer able to move. In Star Trek: Insurrection (1998), Worf is asked why he's aboard the Enterprise-E and away from Deep Space 9; his explanation is literally interrupted. Also, Worf's most notable feature in Insurrection is getting a pimple. For this film, in an earlier script Worf is asked why he isn't too busy with ambassador duties, which were given to him in Star Trek: Deep Space Nine: What You Leave Behind (1999). He drunkenly replies that he was not suited for diplomatic life.
Jeri Ryan (Seven of Nine) had a cameo in the earliest draft of the movie's script. It was scrapped when Ryan got a part on Boston Public (2000). The cameo was given to Kate Mulgrew (Admiral Kathryn Janeway).
The Enterprise Bridge, Ready Room, observation lounge, engine room and some of the corridor sets are the only pre-existing sets to remain from previous films, as sets such as the transporter room, sickbay, and crew quarters were reused from Star Trek: Voyager (1995). For this film, new crew quarters sets similar to the ones seen in the previous film but more detailed, were built, along with a new sickbay and science lab set.
In a deleted scene near the beginning of the film, it is mentioned that Dr. Crusher is preparing to leave for Starfleet Medical. This further adds to the sense of the ship emptying, and further cements this as the final TNG film.
According to his interview in the DVD's special features, Patrick Stewart did all of his own driving for the ARGO scenes, with the exception of the opening shot leaping out of the shuttle and the subsequent sharp turn.
Wil Wheaton (Wesley Crusher) was invited back to the cast by executive producer Rick Berman after Wheaton spoke with LeVar Burton (Lt. Commander Geordi La Forge) on a special Star Trek edition of NBC's The Weakest Link (2001). Wheaton remains in the end titles although all of his scenes were cut from the final version of the film and he can only be seen as a non-speaking extra during the wedding scene.
In one deleted scene, in which Picard and Data discuss the concept of family (and emotions toward family), Data cradles a small flute. The flute is a treasured item of Picard's from Star Trek: The Next Generation: The Inner Light (1992), widely considered as one of the best of the series. In it, Picard lives out another life and raises a family of his own in a condensed, simulated reality. The flute prop was often visible in later episodes of Star Trek: The Next Generation (1987), during scenes in Picard's quarters.
Shinzon's ship, the Scimitar, resembles a lionfish when extending its tines to use its radiation weapon. Picard, for many years, had a lionfish in an aquarium in his Enterprise-D ready room in Star Trek: The Next Generation (1987).
Second time that Counselor Troi assumes command of the Enterprise in a Star Trek movie. The first time was in Star Trek: Generations (1994). Both times, the Enterprise had been (or was about to be) heavily damaged.
The ships backing the Enterprise in Federation territory according to Data (Brent Spiner) and Picard's (Patrick Stewart) meeting in stellar cartography are, USS Intrepid, USS Valiant, USS Galaxy, USS Aries, USS Nova, USS Hood and USS Archer (named for the Captain in the prequel series Star Trek: Enterprise (2001)).
There is a persistent rumor that Michelle Forbes can be seen reprising her Star Trek: The Next Generation (1987) character Ro Laren (who defected to the Maquis) during the wedding reception. It is claimed that she is the dark haired woman seen smiling behind Guinan (Whoopi Goldberg) during Picard's speech. This actress is not Forbes.
The knives used by Shinzon were all designed by Gil Hibben, an American knife-designer who also designed the Rambo III (1988) knife. The knives used in "Nemesis" were not specifically designed for film; all of the designs used are at least ten years old.
The blue beverage seen in the Shinzon - Picard dining room scene is Romulan ale. It is illegal in the Federation because of its highly intoxicating properties. Despite this, Romulan ale has been featured in many Star Trek stories, and possessing it is akin to having Cuban cigars in modern times.
Shinzon is an actual Chinese name, chosen by writer John Logan as it continues the trend of Chinese names for Romulan characters (as well as the new Reman characters). Logan admitted that he has absolutely no idea what the name actually means.
The Argo buggy was designed and built by ProTruck Racing Organization, founded by off-road racing champion Ivan "Ironman" Stewart (no relation to Patrick Stewart). Ivan Stewart appears in one of the DVD special features.
After first reading the script, Marina Sirtis began crying and called Brent Spiner, extremely upset of over the death of Data. Spiner jokingly reminded her that "Data's a fictional character. I'm still alive.".
Scenes deleted from the end of the film would have introduced Steven Culp as Commander Madden, Riker's replacement as the Enterprise's first officer. Culp later appeared as Major Hayes in the third season of Star Trek: Enterprise (2001).