Shinzon's supposedly crooked teeth are straight in some shots, most notably when he conversing with his Viceroy after having dinner with Captain Picard.
A nearly-empty plate of food disappears from the table between shots when Picard and Shinzon have dinner together.
Some "facts" about Picard established in episodes of the TV series Star Trek: The Next Generation (1987) are overlooked or ignored (e.g. in the series, Picard had hair at Starfleet Academy and no longer has his own heart, it having been replaced after an incident there). Altough when Picard is holding a picture of himself at the academy he is shown correctly with hair. The reason why Shinzon is bald might be that he wants to look more like the Remans which he considers as brothers.
There are other elements of discontinuity from the Star Trek series (Worf's transfer to the Diplomatic Corps and Wesley Crusher's resignation from Star Fleet are both ignored and his departure with the "Traveler" during the seventh season), although some of these are explained away in deleted scenes.
At the end of Picard's first meeting with Praetor Shinzon, Shinzon orders the lights to dim back to their original setting; however, the lights begin to dim when he says, "Computer," and before he gives the order for the lights to return to their normal setting.
Guinan is not in the wide shot of the wedding toast. And many of the extras are in different spots in the wide shot compared to the coverage shots.
The orbits of Romulus and Remus as shown in Data's briefing are not possible according to Kepler's Laws of Planetary Motion. The gravitational pull of two planets passing in such close proximity would have eventually dislodged one or both from its orbital path.
Although Shinzon and Picard have identical DNA, speech patterns are not genetic. It is a learned behavior and a product of the environment one grows up in. Although he was probably taught by the Romulan government to speak with a British accent from birth, he more than likely would have become a product of his Reman surroundings and "grown out" of the accent and begun speaking with a similar accent as the Remans or Romulans.
Dr Crusher says that thaleron radiation "has the ability to consume organic material at the subatomic level". This is meaningless. At the subatomic level, all matter, organic or inorganic, is made of identical protons, neutrons, and electrons. Atoms can be organic or inorganic, but they're the same at the subatomic level.
After the collision between the Enterprise and the Scimitar, Shinzon orders his ship to back up, as if they were two cars crashed in a parking lot. The Enterprise remains stationary, which would seem to violate the laws of physics as the Scimitar backs away from the combined wreckage. This is not necessarily a goof. Both ships are at rest when the Scimitar begins to back away. Newton's first law, which respects such things as the mass of the Enterprise, dictates that other than crumpled elements of the ship clinging together (not enough to offset the mass of the Enterprise), the Enterprise would not be pulled along with the Scimitar.
Just as the Scimitar is about to fire upon the Enterprise, Captain Picard calls for the shields to be raised even though the ship has been already at "Battle Stations" status for some time. However, "Battle Stations" means that the crew members are at their stations; it does not mean the shields are up.
During the briefing en route to Romulus, Data advises the Senior Staff about the planet Remus, and he describes Remus as being in a tidally-locked orbit around its sun (meaning one side of the planet always faces its sun) and because of the extreme temperatures on the day side, the Remans live on the dark side of the planet. In a planet that is tidally-locked to its sun like Remus, the dark side would technically also have extreme temperatures as well, on the cold side. The most ideal habitable zones on a planet like Remus would not be the dark side of the planet, but actually the terminator sides (where it transitions from day to night) as temperatures on those sides of the planet would be temperate and optimal for most forms of life. Unless, of course, the Remans had the technology to provide adequate heat, which they appear to have.
Lt. Commander Worf, having been promoted to this rank in Star Trek: Generations (1994), should be wearing the correct rank pips on his collar. However, he is shown throughout the film only wearing 2 pips, his former rank of Lieutenant. Lt Cmdr Worf is, in fact, wearing the three pips signifying his rank as Lieutenant Commander. The third pip is difficult to notice because of his goatee.
During the wedding reception Data refers to jazz as an "archaic musical form", even though everyone in the room seems to be familiar with jazz and is dancing correctly. Even Worf knows who the composer of Blue Skies is. Jazz has been featured prominently throughout TNG's seven seasons, as well as in DS9 and Voyager. However, the term "archaic" simply means old-fashioned, and since Star Trek is set in the 24th century, Data is correct.
After the Argo first jumps from the shuttle and spins around in the sand, Picard's stunt double's face is visible.
Obvious stunt double for Picard during his tumble down the stairs with Shinzon.
During Picard's speech about Riker and Troi you can see a shadow of a pillar on the backdrop of the mountains in Alaska.
During a close up of B-4's eyes, Brent Spiner's real eyes are visible through the contacts.
In the late scene in which Picard impales Shinzon on a piece of the ship, Shinzon then pulls himself forward on the ship piece to get face to face with Picard. However, when the extra portion of the "spear" is shown, briefly, only the tip has blood on it - while the extra portion of the impalement piece (which has also traveled through Shinzon's torso) is blood-free.
In his wedding reception speech Data refers to "Ladies and gentlemen, and invited transgender species." Though a welcome attempt at inclusiveness by writers, this makes no sense as no entire species would identify as transgender, a term referring to a person who identifies differently than the gender they were assigned at birth. A better choice would have been "gender neutral species".
In Unification (1991), Mr. Spock defected to Romulus to aid in the underground reunification movement. In this movie, Shinzon takes control of the Romulan government and appears to make overtures of peace with the Federation, something that Spock would be receptive to. Yet when the Enterprise crew travel to Romulus in this movie, they make no attempt to contact Spock.
In the finale, Enterprise rams Scimitar, breaching the hull at multiple decks and causing considerable damage to both ships. The crash would instantly cause the loss of oxygen, yet the characters continue to breathe without mechanical assistance or even an explanation of why they can still breathe in the absence of Oxygen.
When Dr. Crusher is explaining Shinzon's genetic engineering, she speaks of RNA and DNA in the appropriate instances. However, when she mentions that Picard is the only one with compatible DNA, her lips say "RNA".
When the Enterprise first arrives at Romulus, Picard rises from his chair to walk towards the viewscreen. In the wide shot, the camera pans slightly too far right, revealing the leg and profile of a crew member in street clothes and shoes standing on the bridge.
The observation lounge doors do not line up with the doors that feed into the observation lounge on the bridge. The placement of the doors would send someone right into a wall behind which would be a turbolift car (however in the film the doors lead to a corridor that wouldn't be there).
Throughout the Star Trek history, such importance is placed upon the Prime Directive that a captain would give his life to avoid violating it. Add to this, the extreme measures taken before killing an intelligent life-form by Star Fleet's captains. Yet, when obtaining B-4's body parts, no such concern is shown by firing upon and almost assuredly, killing indigenous people. And, then, openly blasting off revealing advance technology.
The movie takes place after the end of Star Trek: Deep Space Nine (1993) where Worf is given the position of Federation Ambassador to Qo'nos. Yet he appears here in a standard uniform and with no mention of his high ranking position.
Star Trek lore dictates that starships contain one captain and one full commander who has the role of first officer. In this film, the Enterprise is staffed with three commanders, those being Riker, Crusher, and Troi. Should Riker be in command in Picard's absence, the other two could decide to disobey Riker's orders, or if Picard is there, they could all voice different alternatives and end up frustrating him. It seems like this would put an imbalance on the command structure of the ship.
Data states that the inhabitants of Kolarus III are a "pre-warp" society, but yet the Enterprise has no problem with "contaminating" it with its presence in direct contravention of Starfleet's Prime Directive. Not only did the inhabitants see the Argo up close, as well as the Star Fleet personnel, but the Star Fleet crew fired at them, blew up one of their ATVs and possibly killed one or more of the locals. This is an unforgivable lapse on the part of the writers, producers, and director. As for the Enterprise detecting positronic signals, this does not mean that the inhabitants were the source of the technology. The violation of the Prime Directive was serious and flagrant.
During his confrontation with the hologram of Shinzon, Captain Picard states "Your heart, your hands, your eyes are the same as mine." While Shinzon is a clone of Picard and most of this is true because they share the same DNA, Picard actually has an artificial heart. It was established on Star Trek The Next Generation that he lost his biological heart as a cadet when he was stabbed through the heart by a Nausicaan. However, Picard's statement was meant to be more poetic than literal.
Riker recalls his first meeting with Data as being on the holodeck trying to whistle. However, in Encounter at Farpoint (1987), they actually met and spoke to one another on the battle bridge in an earlier scene. That said, not being formally introduced to Data, he may have forgotten this exchange.