Revealing mistake: When Qui-Gon is attacked by Darth Maul for the first time, he escapes by leaping onto his ship which quickly takes off. As they zoom up into space, he discusses the mystery attacker with Obi-Wan. However, the lighting from outside the windows never changes giving the impression that they are static on a set rather than whizzing up into space.
Continuity mistake: After Qui-Gon is struck by Darth Maul's lightsaber, he drops down, and his lightsaber is lying on the floor. In the shot where Maul turns around to face Obi-Wan, the sabre is not lying in the same place as before (seen from the colours of the floor), and the activation button faces upwards, which it didn't do in the previous shot. In the next shot of Qui-Gon, his lightsaber is now closer to him than in the previous shot.
Audio problem: When Obi-Wan rushes through the Force Doors, after Qui-Gon's death, to face Maul, watch and listen carefully. Obi swings his lightsaber three times in rapid succession, Maul blocks all three attacks. The lightsabers appear to contact, there is even the almost subliminal flash from the beams hitting each other, but the sound crew only inserted two contact sound effects, and those two sounds are slightly out of sync with the actual movements.
Continuity mistake: Near the beginning of the film, there's a few shots of the droid army landing on Naboo, with one shot of one of those hover tanks moving out of the landing ship towards the camera. In front of it are three droids in a line who are also walking towards the camera. Unfortunately, the tank is moving much faster and is bearing down on the droids with no sign of stopping - unfortunately the shot changes just before it runs them over. (00:09:55)
Deliberate mistake: When Obi-Wan is fighting Darth Maul alone, after Obi-Wan cuts Maul's lightsaber in half, they start fighting on a different side of the pit. But after Maul kicks him, a close-up of Obi-Wan shows the wall and smoke of the area that they left. The shot has been reversed as well. The easiest way to see this is to watch his braid, which is on the wrong side. (01:56:55)
Continuity mistake: After the final battle scene when the Jedi council come down to the Naboo city, as they are leaving the space craft there is a figure in the background who is obviously supposed to be Mace Windu, but is definitely NOT Samuel L. Jackson. The man is African-American, bald and dressed in Windu's clothes, but is not him. Perhaps Mr. Jackson was unavailable that day. (02:00:50)
Continuity mistake: Just before the podrace Qui-Gon talks to Shmi on the platform. After the conversation, they walk towards the camera. Pay attention to the background, it's the same as the previous shot even though Qui-gon and the others are walking in the other direction.