- Continuity: 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). 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.
- Continuity: A nearly-empty plate of food disappears from the table between shots when Picard and Shinzon have dinner together.
- Audio/visual unsynchronized: 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".
- Revealing mistakes: After the Argo first jumps from the shuttle and spins around in the sand, Picard's stunt double's face is visible.
- Revealing mistakes: When Data is standing next to the computer during the briefing about Remus and Shinzon, a reflection of the green screen backdrop beyond the briefing room windows is visible.
- Revealing mistakes: During Picard's speech about Riker and Troi you can see a shadow of a pillar on the backdrop of the mountains in Alaska.
- Continuity: Shinzon's supposedly crooked teeth are straight in some shots, most notably when he conversing with his Viceroy after having dinner with Captain Picard.
- Continuity: 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.
- Continuity: Troi's hands shift between shots during the attempted rape.
- Continuity: In Picard's quarters near the end of the film, the way Picard holds his wine glass changes from shot to shot.
- Revealing mistakes: Obvious stunt double for Picard during his tumble down the stairs with Shinzon.
- Errors made by characters (possibly deliberate errors by the filmmakers): Lt. Commander Worf, having been promoted to this rank in ST:Generations, 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.
- Continuity: 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.
- Crew or equipment visible: 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.
- Factual errors: 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.
- Incorrectly regarded as goofs: The Remans board the Enterprise on the lowest deck where the shields are down. Yet several scenes later the Viceroy falls the height of several decks despite supposedly being on the most bottom deck. However, the Remans were likely to ascend several decks in their search for Picard. Some of the signs on the surrounding doors even show they are on a deck higher up then the lowest one.
- Continuity: When the Argo jeep jumps from the shuttle, Picard and Data are not wearing the eye protection goggles as they are are just moments latter.
- Incorrectly regarded as goofs: Just as Shinzon's ship is about to fire upon the Enterprise, Capt. 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.
- Continuity: In First Contact, Picard says that the Enterprise-E had 24 decks, but in Nemesis the intruder alert is on Deck 29.
- Errors in geography: While fighting Commander Riker on board the Enterprise, the Reman Viceroy plummets through an endless white chasm to his death. An endless chasm on board a spaceship? This should likely be damage to the ship's decks, but the decks/damage are not shown at all.
- Errors in geography: During Data's briefing, we see Remus as being in an outer orbit compared to Romulus. But in a later surface shot of the Reman mines on the dark side of the planet, a sunlit Romulus appears in the night sky, implying that Remus is in the inner orbit.
- Plot holes: 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 Star Trek's Prime Directive.
- Factual errors: The orbits shown 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 long ago dislodged one of both from its orbital path.
>>> 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.
- Revealing mistakes: SPOILER: When Shinzon makes his final lunge at Picard, the piece of ship Picard uses to impale Shinzon can be seen to shift laterally across Shinzon's chest, an impossibility if it had impaled him through the chest.
- Revealing mistakes: SPOILER: "Dead" Shinzon can be heard grunting when Data pushes him aside.
- Factual errors: SPOILER: To separate the ships, the Scimitar goes into reverse, but the Enterprise does not. Physics states that without an equal-but-opposite reaction (i.e. putting the Enterprise into reverse as well, or some other form of resistance) the Scimitar would just pull the Enterprise with it instead of pulling them apart.
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