Revealing mistake: When Amidala and Anakin are eating and he cuts her a piece of the fruit and "floats" it back to her, the bite appears in the fruit a split second before she actually eats it. [This appears to be fixed in rereleased versions]. (00:53:40)

Plot hole: When Amidala and some of the clone troopers get blown out of the ship chasing Dooku, later the trooper approaches Amidala and asks about making their way back to the front lines, but Amidala says they should go to the hangar to help Obi-Wan and Anakin. How did she know about the hangar, having left the ship quite some time before it arrived at the final destination? (02:05:50)
Other mistake: How is it that one slash on Amidala's back ripped off the entire midriff of her shirt, and a sleeve? (01:47:00)
Trivia: The first scene in which Obi-Wan and Anakin appear was filmed after principal photography had finished. Ewan McGregor had shaven off his beard, so he had to wear a fake one.
Trivia: When Anakin is walking around the bar in Coruscant looking for the changeling, he passes Ahmed Best, the voice of Jar Jar Binks, and we also see Anthony Daniels, who plays C-3PO. Katie Lucas (George Lucas' daughter) is also visible.
Trivia: Nearly every single Clone Trooper is computer generated.
Obi-Wan Kenobi: [To Anakin.] Why do I get the feeling you're going to be the death of me?
Junkie: Do you wanna buy some death sticks?
Obi-Wan Kenobi: You don't want to sell me death sticks.
Junkie: I don't want to sell you death sticks.
Obi-wan Kenobi: You want to go home and rethink your life.
Junkie: I want to go home and rethink my life.
Obi-Wan Kenobi: If you spent as much time practicing your saber techniques as you did your wit, you'd rival Master Yoda as a swordsman.
Anakin Skywalker: I thought I already did.
Obi-Wan Kenobi: Only in your mind, my very young apprentice.
Question: When Anakin and Padme get married, Anakin is wearing an outfit that is often seen on Jedi and is displaying a Jedi Padawan's hair braid. Do he and Padme not care that the man who performs the wedding is seeing him (as Jedi are not supposed to have relationships and marry)? Why not disguise him? It's a huge risk to let even one person see a Jedi getting married.
Question: The lightsaber Anakin wields in this film is described as being his first lightsaber, so why does he say "Not again!" when it's destroyed in the Geonosis factory?
Question: After the clones were discovered, Palpatine used the Separatist-Republic tension as a excuse to take control of them, but was the Separatist movement real? He could've faked it from the beginning just to take the clones out himself knowing that he would have power because of the senate. Or was the movement real at first, and he later used it to take control of the clones? The attempt on Padmé's life (which caused the Kamino reveal) besides being the price that the Viceroy requested to enter the Separatists I suppose, was to provoke the war, what do they achieve then, if they didn't know the clones would be discovered?
Chosen answer: Palpatine was playing both sides. As Sidious he was controlling and helping the separatists (which sprung from the actions of the trade federation) and as Palpatine he was defending the Republic. Both sides did not know they were being played and both sides thought their cause was "real".
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Answer: Agolerga, who officiated the wedding, would have known who both people were, especially Padme. Remember they were also keeping the marriage secret because of Padme's position as Senator. Assuming Agolerga was aware a Jedi can't marry, he may simply not care or agree with the rule. Also, as a holy man of Naboo, Anakin and Padme may have trusted him with their secret.
Bishop73