When Qui-Gon and Obi-Wan are talking to Jar Jar when they first arrive on Naboo, Obi-Wan's hair is wet. When Jar Jar spins around and Obi-Wan is forced to duck, his hair suddenly becomes dry. In the next shot it is wet again.
After Daultay Dofine's first line of dialogue ("I knew it! They're here to force a settlement!"), he and Rune Haako switch voices. For the rest of the film, Haako speaks with Dofine's voice, and vice versa.
Before Anakin shoots down the Destroyer Droids in the Theed hangar with the Naboo Starfighter, his mouth is shown moving before he says, "No, wait, here it is" while referring to the starfighter's laser cannon trigger.
After the transport is destroyed in the hangar (near the beginning of the film) the scene cuts to Obi-Wan and Qui-Gon. The sound of their lightsabers being activated occurs before they even draw them from their belts.
Tey How says, "Sir, we're losing power. There is some problem with the main reactor... ." When Captain Dofine replies, "Impossible! I don't... .", his lips don't move until he is almost finished speaking. When they move, he appears to be saying "Impossible... ."
As Qui-Gon is weighing his options for payment, Anakin states, "there's a big race tomorrow..." However, the race is the day after tomorrow, as Anakin spends the next day getting his pod ready for the race and another evening follows.
After Darth Maul is chased into the large room with the chasm by Obi Wan and Qui Gon, he backs off to the edge and the camera goes back to a more distant angle. At that moment Darth Maul seems to almost stumble into the chasm and quickly catch himself again.
During the final lightsaber battle, the red force fields can be regularly seen opening and closing before Obi-Wan emerges from them. After he does, they cannot be seen or heard opening or closing again.
In the Nubian parade scene at the end of the movie, Anakin Skywalker is seen as a Jedi Padawan and sports a new haircut and a Padawan braid. The braid is considerably longer than his hair had been at any other point in the film.
When Anakin and Padme arrive at the pod racer hanger, Anakin is taller in the close-up shots, and Padme's hair is noticeably a little different. The close-up shots were done almost a year after the principal photography.
At the beginning of the Battle of Naboo, the Gungans create a shield around themselves using a number of shield generators on the backs of their mounted creatures. In a later scene, only one of these creatures has a shield generator on its back.
In the final fight scene with Obi-Wan and Darth Maul, Obi-Wan
leaps up from the hole, and grabs the lightsaber with his left hand. As he twists above Darth Maul's head, the lightsaber is in his right hand, when he lands, it's in his left hand again.
During the final fight between Obi Wan and Darth Maul, Maul force pushes Obi Wan into the pit. For the wide shot Maul is seen using his left hand to do this, but for the close up he is using his right hand.
During the fight over and around the droid control ship, Anakin says to R2D2, "I'll try spinning, that's a good trick." Anakin is seen to turn the flight controls to the left, but his craft spins to his right. In an earlier scene (right after the auto pilot is disconnected) Anakin says, "Let's go left", turns the controls to the left, and the scene tilts to Anakin's left, showing that the controls are working backwards in one of the two scenes.
When Qui-Gon and Obi Wan are waiting for Jar Jar to get help from the Gungans we see shadows and light on their faces from the leaves on the trees. These shadows move constantly. In the close upos, they are entirely in shadow and there is no light showing through.
In the scene where Qui Gon is cutting through the door aboard the trade federation ship, two destroyer droids roll along the corridor towards them. Both droids are seen to deploy blue energy shields as they unfold; however, when Obi-Wan makes his comment about them having said shields, the camera cuts back to a brief shot of the two droids, during which the droid nearest the camera is seen re-deploying its shield.
When the Gungan army's front line of solders pull out their personnel deflector shield rims they all switch them on. This fills in the rims with a blue light. A few moments later looking out from behind the army's front line you can see the personnel deflector shield rims but not one is filled in with blue light.
When Senator Palpatine and Queen Amidala are on Coruscant discussing their options regarding the senate, Palpatine is wearing a blue outfit. As he walks around the room, the same outfit changes from blue to brown then back to blue as he finishes the conversation.
Just before Anakin's pod-racer gets stuck with Sebulba's, he is on Sebulba's right side. When they get stuck together in the next shot, Anakin is suddenly on Sebulba's left side without having changed positions.
The droid army is entering the city it cuts to the scene where the Queen is looking out of the window in her palace. As it shows her approach the window you can clearly see a large ILM (Industrial Light & Magic) sign written in what looks like red spray paint at the bottom right hand corner of the screen.
When Queen Amidala is standing before a big window (she watches the Trade Federation enter the city) she is wearing a dress with lights at the bottom. Behind her the power cable of those bulbs is visible.
When the engines start turning on Anakin's pod racer, they are turning the wrong direction. They should be turning so that the fan blades will force air into the engine, but the direction they are turning, air will blow out the front of the engine.
Many naturalists complained that Watto's wings weren't big enough to lift his body in flight. George Lucas explains that Watto's digestive system filled his rotund belly with helium, making Watto a blimp, not a bird.
When listing candidates for Chancellor, Captain Panaka includes "Bail Antilles of Alderaan." Some viewers think he means Bail Organa of Alderaan (played by Jimmy Smits in later movies). However, there is nothing unusual about two men from the same province having the same first name. The script explains that these are indeed two different characters.
As Qui-Gon, Padme, and R2 enter Anakin Skywalker's home Qui-gon introduces himself to Anakin's mother. As Qui-Gon says, "I'm Qui-Gon Jinn", Padme mouths these same words. This might not be visible in the pan and scan version of the film.
When Darths Maul and Sidious are conversing on Coruscant ("At last we will have revenge!"), Maul's neck is visible beneath his cloak, and is flesh-toned. Everywhere else in the film, his neck is black.
When Qui-Gon and Jar Jar are eating the meal at Anakin's house, his mother goes around the table pouring water into everyone's cups. She pretends to pour it into Jar Jar's computer-generated cup, and it sounds as if she does, but no computer-generated water has been added into the scene.
When Jar Jar Binks is leading Qui-Gon Jinn and Obi-Wan Kenobi to the underwater city, Qui-Gon Jinn asks, "How much further?" to which Jar Jar Binks states they must go under water. Qui-Gon Jinn and Obi-Wan Kenobi make motions to get out breathing apparatus but it can be seen that they have been carrying them in hand for the entire scene, even before finding out the city was underwater.
After R2-D2 repairs the shield generator, there is a scene where Padme is cleaning up the droid and talking to Anakin. In the last shot of this scene, the film is reversed (mirror image) - evident from R2-D2's features.
When Qui-Gon delivers the hyperdrive, Obi-Wan's braid is on the left side and not the right. Evidently, this was done deliberately with the intention that the shot would later be flopped, but for some reason it never was, leaving the braid on the wrong side.
Senator Palpatine and Viceroy Nute Gunray are about the same height, and Darth Maul taller than both. But in one scene while Nute Gunray is sitting and Darth Maul is standing next to him, Darth Maul appears much shorter than usual.
A green Landspeeder similar to Luke Skywalkers in Episode IV is visible when Qui-Gon's party enters Mos Espa. It should be floating above the ground, but two of it's three wheels are visible, despite two black clad humans standing in front of it trying to cover up the wheels.
In the final scene of the movie, you can see a girl in a peach colored dress standing behind R2-D2 and Anakin. A few shots later, she is seen in the foreground of a shot of children throwing confetti down onto the parade. A few shots later she is back behind R2-D2, Anakin, and the Queen.
After the Trade Federation is defeated, Padme's decoy is again playing the role of Queen Amidala when she is speaking to the Viceroy after their defeat, even after Padme revealed herself to the Viceroy as the real Queen Amidala in the throne room.