Revealing mistake: When Amidala & 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.
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?
Audio problem: The aliens that populate the planet of Geonosis have an extremely peculiar method of speech - consisting of clicks and weird ringing sounds. However, despite the fact that they make up 99.9% of the crowd in the arena, the sound of the crowd cheering is human.
Other mistake: How is it that one slash on Amidala's back ripped off the entire midriff of her shirt, and a sleeve?
Continuity mistake: When Padme gets her back scratched she seems to bleed. Even though she is wearing all white, and the scratches seems to be deep, her white top remains squeaky clean during the rest of the movie and does not get dirty from her wound.
Audio problem: When Anakin and Padme are talking after their meal together. When the camera is facing Anakin at one point he says "Believe me I wish that I could just wish away these feelings I have for you!" and then stops talking. When the camera switches to face Padme, if you watch closely, Anakin's mouth is still moving even though he isn't saying anything.
Continuity mistake: During the sequence where Obi-wan goes to meet Yoda regarding the absence of Kamino from the Jedi Archives, look closely at the collection of children Yoda is training. While most are human, there is one that is alien, with a reptilian face of dark skin. He sure moves fast, because at first he is at the back in the centre of the group of trainees, in the next shot he is at the front of the group of trainees, and by the end of the scene, he is on the far left, yet we never see him, or any of the other children, move.
Continuity mistake: In the arena scene, you will notice that Padme's hands are chained to the pillar and pulled up above her head. The chain is taut. However, subsequently the chain becomes sufficiently slack for Padme to bring the cuffs to her mouth and unpick it.
Continuity mistake: Right after Zam's speeder crashes near the bar and Anakin is chasing her through a crowd it shows a shot of him running really fast through the crowd. Then it cuts to her and back to him. When it cuts back to Anakin it is the exact same shot as the previous one. (You can tell because he passes a bright yellow light and then he puts his left hand on someone's shoulder as he passes them. All this repeats on the second shot.)
Continuity mistake: In the arena scene, Anakin's pillar already has a chain hanging from the top before he is led to it, however, when he is led to the pillar, the chain is no longer there, and a new one is hoisted to the top by the flying Geonosian guard.
Continuity mistake: During the scene when Obi-Wan attempts to capture Jango Fett as he departs Kamino, Fett and his son Boba can be seen about to load crates onto his ship. As soon as Boba warns Jango about Obi-Wan's presence, Jango tells Boba to get in the ship, the scene switches view, the fight between Jango and Obi-Wan starts and where did the crates go?
Continuity mistake: When Anakin and Padme are about to eat, Anakin uses the force to levitate her pear-like fruit to his plate. He then proceeds to cut it pretty much in half. However, the piece he sends over to her is much smaller than half - we even see the remainder of the pear on his plate which is substantially larger than it was in the shot before.
Continuity mistake: The twin-engine speeder which Anakin is using to pursue Zam is equiped with four antennas, two of them between the headrests. In the shot when Anakin is trying to catch the falling Obi-Wan, the two antennas in the middle are missing.
Revealing mistake: When Padme and Anakin enter the droid production centre, there is a shot of them going through a large door. Though they both crouch slightly, Anakin's head passes through the door.
Other mistake: After getting off the airspeeder at Naboo Padme and Anakin walk down a long balcony. R2D2 behind them has a huge dent visible on his dome. How did that happen? Did he fall down the stairs at some point?
Continuity mistake: When Palpatine is speaking to the Jedi very near the beginning, the ships in the suspended invisible freeways on the background are always going on the same pattern. Notice that there is an elongated ship with a large rear tip, and then two smaller ships always seem to catch it at the same time. This goes on for about 3 minutes.
Continuity mistake: When Anakin and Padme are standing outside the Lars' house, we see their shadows projected on to the side of the house (with Anakin's shadow looking worryingly like Darth Vader's). However, in the next shot their shadows have moved about 4 feet to the left, and the shadows on the ground also change size and intensity between shots several times.
Continuity mistake: When Padme is packing to leave with Anakin for Naboo, she has a pink outfit in her hands, and she starts walking towards her suitcase. The shot changes and she is still walking, but the pink outfit has been replaced by a navy blue one.
Continuity mistake: When Ani purposely jumps out of the speeder to catch Zam, in the same shot he does this, Obi-wan switches to the driver seat and you can see he has blue jeans on. All other shots show him wearing tannish pants.
Revealing mistake: During the scene at the dinner table with Anakin and Padme, Anakin makes a piece of fruit fly around. He then has it land on a plate and cuts it with a fork and knife. It happens fast but you don't really even need slow motion or pause to see that the fruit doesn't react to Anakin sticking his fork or knife in it at all. The knife and fork just vanish into the fruit.