- Continuity: MacLeod (doesn't) lean out of the car at the prison complex.
- Continuity: When Juan Sánchez Villa-Lobos Ramírez was killed in the prison he had the Samurai sword with him and Connor MacLeod runs out of the prison with his other sword. In the final fight Connor MacLeod has the Samurai again.
- Continuity: MacLeod's sword changes from a broadsword to a shortsword several times during the last fight.
- Incorrectly regarded as goofs: Katana has knowledge of league draft rules and the Wizard of Oz, despite never having visited Earth, but he has a screen he uses to monitor McLeod, so he could have learned about them through it.
- Continuity: When Katana is "beamed" to Earth, he is not wearing gloves. When he arrives on Earth, he is wearing them.
- Continuity: MacLeod's jacket keeps switching from a black bomber jacket to a full length coat during the final 20 minutes of the film.
- Continuity: The Highlander fights a villain on top of a train. During the fight the train drives through a waterfall, forcing the villain to take off his sunglasses. He gets his head cut off, but the loose head is wearing sunglasses again.
- Plot holes: Ramirez and MacLeod enter the prison with a car. The guards shoot the car with machine guns from all sides. But MacLeod's friend Louise Marcus, in the trunk of the car, not only survives but is even unhurt.
- Crew or equipment visible: In the fight scenes in the beginning of the movie, the lines suspending the actors in the air are clearly visible.
- Continuity: Louise Marcus swims into the Shield Corp., pulls off her scuba hood and mask, and has a immaculate hairdo and makeup.
- Continuity: Katana brushes his coat against the shield energy and loses a piece, but for the rest of the scene it's intact again.
- Continuity: During Connor and Katana fighting around the shield energy they destroy several railings, but then after Katana burns his hand they are all intact again.
- Revealing mistakes: When Katana throws Blake out of a window the dummy that hits the ground is very, very obviously a dummy.
- Continuity: A fire escape that McLeod uses to reach the ground is seen rising up twice in consecutive shots.
- Continuity: Juan Sánchez Villa-Lobos Ramírez is admiring himself in a wall of monitors just before getting fitted for his new suit. A pedestrian walks in between Ramírez and the camera but does not show up on the monitors.
- Factual errors: In the Renegade version, the closing credits list Bruno Curichelli as "Zeist Chief Justice" even though the film has eliminated the whole Planet Zeist angle from the film.
- Revealing mistakes: When the subway car is speeding out of control there's an obvious dummy blowing around in a quick shot of the scene.
- Factual errors: Error in depicted physics - Law of Acceleration - the subway Katana hijacks is traveling at over 400 MPH (KPH) when it crashes through the wall, yet stops only a few feet from the impact point. Additionally, the subway system would have protective barricades inside the subway or tunnel to prevent the crash from occurring, let alone being capable of reaching such ridiculously high speeds.
- Revealing mistakes: Support wires to the flying device used by one of the villains fighting MacLeod after he has left the bar are visible.
- Continuity: When Louise and MacLeod get out of the truck towards the end to climb the mountain, she is wearing different clothes from what she was wearing when they were fighting Katana.
- Revealing mistakes: Obvious spark generators in front of the subway when Katana is driving it at high speed.
>>> 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 Ramirez is killed, his sword is left behind with him by MacLeod, yet he has it for the final fight with Katana.
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