Other mistake: When the star ships are about to pass through the clouds over Coruscant in the beginning of the film, the shadow of the large Naboo Cruiser can be seen far ahead of the ships, but the smaller star fighters have no shadow. And when the ships fly closer to the clouds, the shadow of the cruiser disappears as well.
Other mistake: After Padmé falls down onto the conveyor belt, Anakin jumps down after her, and right before he lands, there's a clear shot of the conveyor belt moving the same way Padmé went. Judging from the speed of the conveyor belt and the fact that she was only a few seconds ahead of Anakin, Padmé should be visible, but she's nowhere to be seen.
Other mistake: When Padmé is trapped in one of the vats that get filled with molten metal, the vat two spaces ahead of her is filled up twice once after Anakin's arm gets stuck, and once as the flying R2-D2 comes to save her. Then, as Artoo lands, Padmé's vat moves one step closer to the metal-pouring mechanism, and the vat next to her is just about to get filled up. But about ten seconds later there's an overhead shot, and molten metal is being poured into the vat next to Padmé's, even though the vat, and Padmé's vat as well, should already have been filled up by the time given.
Other mistake: When Obi-Wan goes to the water planet and talks to the Prime Minister in his office. The alien is of course computer generated. When the actors do their blue screen work, markers are put up for them to look at so that when the finished shot is done, and the alien is put in, it looks like they're looking at the alien. In this scene, Obi-Wan is clearly not looking at the alien. (On one of the "making of" trailers at starwars.com you can hear George Lucas jokingly say "Eye-lines! I don't care about no stinking eye-lines," and the scene behind him is Obi-Wan talking to the alien...)