Other mistake: The battle droids - including the commando droids featured here - habitually have two broad fingers and a thumb. So how can a commando droid squeeze itself completely into clone trooper armor without its broad fingers tearing open the gloves, since it can't separate its fingers?
Deliberate mistake: At the beginning, Asajj Ventress is wearing an outfit with a long skirt. When she is rescued from her damaged starfighter by the scavengers, the skirt has vanished. This was done because the animators found the skirt too difficult to animate. This is also why she receives a brand new outfit that never had a long skirt later in the episode.
Plot hole: When Lawquane spots the droids in the field, he identifies them instantly as commando droids. But as he had left the Republic Army shortly after the first battle on Geonosis (the one which started the war) and has lived as a farmer ever since, and since the commando droids are relatively new (see "Rookies"), how can he know what they are? With his lack of battlefield experience, he should simply call them battle droids.
Continuity mistake: After the droid advance force has split up to hunt down Master Yoda, the Jedi Master and his clone escorts attack each group on their own. When Yoda ambushes his group, it has six battle droids; but he is seen finishing only four of them. The remaining two just vanish from the scene.
Continuity mistake: During the end scene, when Echo and Fives are honored for their services, in the first shot, Echo's helmet is missing, despite his arm being positioned as if he's holding it. When his helmet appears, it's missing the red binocular attachment, which only appears later in the scene.
Continuity mistake: After Grievous has received R3's message, he assures the dismembered R2 that he will not come to harm. We see R2's head lying on the dissection table with his electronic eye dangling from a cable. But when Grievous stands up again, just before his Magnaguards enter, R2 has his eye back in place. It's a brief shot, so you'll have to be quick to catch that glitch.
Other mistake: During Padmé's big speech to the Senate, Duchess Satine is visible in the background watching at one point. Satine is the ruler of Mandalore, a neutral planet, not a Senator, and thus has no reason to be present at a normal session of the Galactic Senate.
Continuity mistake: When the two factions of Hondo's pirates are fighting each other, the ones who sided with Maul and Savage are using blasters that fire red bolts, while the ones that stuck with Hondo shoot blue bolts. When Hondo persuades the traitors to work for him again and they attack the two Sith, all of the pirates' blasters are now firing blue bolts. This is Star Wars, not G.I. Joe, and weapons don't just change colour like that.
Continuity mistake: In the previous episode, the Republic troops blasted huge holes into the Separatist lab to enter it. In this episode, in which the highly contagious airborne virus is unleashed into the facility, the holes are conveniently nowhere to be seen, so it can't get loose onto Naboo.
Continuity mistake: Rex's kama (the black kilt-like thing he wears) is missing twice: first when he, Anakin and Ahsoka are looking at a hologram of an AT-TE on the Resolute's bridge, and second when Anakin's trap for Grievous is revealed, and Rex orders the AT-TEs on the asteroids to fire.
Continuity mistake: After the shuttle has crashed, there are four surviving clones accompanying Jar Jar. When they run from the acid geyser, there are only three clones with Jar Jar, but later on, when they chase down the Weequay pirates, there are again four clone troopers.
Continuity mistake: After Yoda cuts a hole in one of the droid battle vehicles, and throws the droid out, the following scene returns to Asajj and the Toydarian king. When their backs are shown, Asajj is standing close beside the king, but in the very next shot (showing them from the front), she is obviously a few feet farther from him.
Continuity mistake: At the beginning of the queen's audience with Count Dooku, when he says, "But I was invited - by your faithful advisor. He's concerned over how attached you've become to Skywalker," there is a shot of Dooku walking up the room, then it cuts away to the queen and Atai Molec (the advisor in question), and when it cuts back to Dooku, he walks through the same part of the throne room as in the previous shot of him. Take note of a screen on the side of the room - it's in the same position both shots.
Continuity mistake: When Anakin is cutting through the door of the Kadavo facility after Master Plo's forces have arrived, the position of the hole he's making is different from when it was previously shown. When he finishes cutting the hole and kicks in the cut-out section of door, the hole is back in its original position.
Continuity mistake: Anakin sends a ship to dock with Aayla Secura's stricken Jedi Cruiser to pick up everyone who's escaping. When the ship docks, there are two clone pilots flying it. When the ship is damaged by Separatist fire while attempting to dock with the Resolute, causing its hyperdrive to activate, one of the pilots is killed due to the damage, but the other pilot has vanished.
Continuity mistake: Rex climbs onto a barrier of pods that the Jedi built in front of the village to take a look at the approaching droid forces, and reports that they have eight minutes tops before the Separatists' arrival, prompting Anakin to order the shield generators put in place. Cut to General Lok Durd and his chief battle droid, who look through binoculars at the distant village, where the barrier is shown as incomplete, with Ahsoka and Aayla still moving pods into place.
Continuity mistake: After landing the Separatist shuttle at the Lurmen village, Anakin, Ahsoka and Aayla get out and walk around the shuttle, underneath its legs, toward Tee Watt Kaa and Wag Too, as Aayla announces that the Separatists will arrive in moments. When she's finished speaking, the three Jedi have emerged from underneath the ship. The scene cuts to Tee Watt Kaa demanding to know why they came back, and when the scene cuts back to a close-up of the three Jedi, they're walking out from underneath the shuttle again.
Plot hole: When Ahsoka rushes to save the students when they arrive to meet the prime minister, she kicks the secret service agent, however we see her standing next to the prime minister acting innocent. The agent she kicked to save the students would have no doubt told the prime minister right away that Ahsoka stopped them, and the prime minister would know which side she was on.
00:11:55 - 00:13:40
Continuity mistake: When Anakin and his men rush to aid Obi-Wan in the south tower, about half a dozen droids marching inside separate the two Jedi. Anakin begins cutting them up; one of the droids is already crossing the threshold. But when Anakin finally reaches Obi-Wan, the droid who has already entered is suddenly no longer present. The hips and legs falling in before Anakin rushes in come from another droid just outside the door.