Audio problem: When Obi-Wan rushes through the Force Doors, after Qui-Gon's death, to face Maul, watch and listen carefully. Obi swings his lightsabre three times in rapid seccession, Maul blocks all three attacks. The lightsabres appear to contact, there is even the almost subliminal flash from the beams hitting each other, but the sound crew only inserted two contact sound effects, and those two sounds are slightly out of synch with the actual movements.
Audio problem: After Obi-Wan and Qui-Gon are greeted by TC-14, as they're walking over to the windows, Obi-Wan says, "How do you think the Trade Federation will deal with the Chancellor's demands?" His mouth is visible as he says the last word, and even though he's far away, you can see that his lips are not moving. (00:03:25)Kylantha
Audio problem: When Anakin and Qui-Gon are running to Amidala's ship, Anakin says, "Qui-Gon sir, wait, I'm tired" but his lips hardly move when he says this. (01:13:35)
Audio problem: When Obi-Wan and Darth Maul are fighting, after the second time Maul swing his lightsabre over Obi-Wan's head, their lightsabres make contact three times, but there are four clashing sounds. (01:56:35)
Audio problem: Where Natalie Portman and some of the security detail are fighting in the Palace corridors, her shiny weapon makes a distinct noise and the normal blasters makes a different sound. Later, she is given a regular blaster to get up the outside of the Palace. However, when she fires that gun to break the window they've ascended to, it makes the same noise as her shiny blaster, not the sound of a normal blaster. (01:50:31)
Audio problem: When Queen Amidala shows the holographic map of the palace and discusses the plan for sneaking into it, you can tell that her explanation of the plan is a recording. There is one shot where you can see her face and her lips are not moving.
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.