Continuity mistake: During the funeral pyre scene, the folds in Obi-Wan's hood change between consecutive shots.
Continuity mistake: When Palpatine and Queen Amidala address the Senate, the holocam flying around near them is inconsistently placed between shots.
Continuity mistake: When R2-D2 and three other astromech droids fixing the Nubeing ship, Jar-Jar is talking to them and there is a black one. This black one turns into a blue one when they are fixing the ship. It's the second one to get blasted.
Continuity mistake: During the climatic light-saber duel, just as Qui-Gonn and Obi-Wan have forced Darth Maul onto a ledge, look quickly and you will see that the red blade of Maul's light saber goes from being behind his waist to in front of it between shots.
Revealing mistake: When the Gungan army set up their shield at the Naboo plains, you see the Trade Federation tanks coming over the hill. When the camera turns to behind the tanks, you see the bottom of one of the beige tanks disappear slowly.
Continuity mistake: 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.
Continuity mistake: After Obi Wan halves Darth Maul, his lightsaber is in his hand as his body falls downward. Next shot is overhead and no saber is in hand or plummeting down the shaft.
Audio problem: When the Viceory and his assistant talk, most of the time their mouths don't match their words.
Continuity mistake: The shadows change angles all over the movie. First the shadows appear right beneath the characters, then in the next clip they are cast with an angle. And the shadows that ships and computer-animated animals cast are different from the "real" characters.
Continuity mistake: When Anakin says his last words to his mother, she is closer to the door than in the previous shot.
Other mistake: Darth Sidious orders the Droid army to kill all Gunguns in the battle in the field, but as the battle ends, the droids order all Gunguns to drop their weapons, and do not kill them. As robots, they should follow simple orders.
Revealing mistake: In a few of the wider crowd shots during the pod-race, you can make out some oddities. In particular, if you look closely, you'll see the same group people copy/pasted over and over in different places and different configurations in the audience to make the crowds seem bigger. (Slow motion or pausing helps, but is not necessary.) This is actually a relatively common special effects trick to make crowds seem bigger.
Revealing mistake: In the final celebratory parade/ceremony scene, sun/shadow angles vary drastically between shots and a variety of items (flags for example) cast no shadows at all.
Continuity mistake: At the start of the lightsaber fight in the hanger all three go through some large doors and into the big generator room. Behind them a set of stairs have appeared.
Continuity mistake: When Obi-Wan runs towards Darth Maul and Qui-Gon he is halfway down the walkway, but when it cuts to Darth Maul and Qui-Gon Obi-Wan is now at the far end.
Audio problem: When the droid army are marching into battle at the end we hear a marching army, but they're walking on grass and the sound should be muffled in some way.
Audio problem: 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.
Continuity mistake: When Obi-Wan is hanging from the ledge in the abyss after Darth Maul knocks him into it, he sees Qui-Gon's lightsaber a distance from him and uses the force to grab it. Between shots, the lightsaber changes position on the floor.
Answer: The entire time Palpatine is bitching to Viceroy Gunray that he needs the Queen to sign the treaty to make the blockade and invasion legal. He didn't send Darth Maul to kill Amidala, he sent him to capture her and to deal with her Jedi escort.
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