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: When Ahsoka leads a captive Cato to Jocasta and asks if she's all right, before they head off to call security, Ahsoka's lightsaber is absent from her belt in the first shot, but present in the second. (00:20:31)
Continuity mistake: The opening scene after the narration shows the end of "Cargo of Doom" again, focusing on the clone troopers, but the details are different, including Anakin and Ahsoka disembarking the shuttle with R2 and some of the clones removing their helmets before leaving, when that didn't happen in the previous episode.
Audio problem: When Anakin says, "What? Uh-oh," his mouth does not move. He just looks shocked that his lightsaber could not cut The Zillo Beast.
Other mistake: Obi-Wan Kenobi discovers the Mandalorians and gets into a fist fight with them, punching one in the face a few times, who reacts with obvious discomfort. But the one hit is wearing Mandalorian armour, famously resistant to all kinds of weaponry, and Obi-Wan is barehanded! The Mandalorian should be laughing off his attempts. Not to mention that later he surprises another armed guard in Mandalorian armour and knocks him out with two barehanded blows to the helmet.
Suggested correction: It must be pointed out that unlike the Mandos he's fighting, Obi-Wan explicitly has supernatural powers, powers that most certainly help with things like punching out people in full armour. Seeing this as a "mistake" is kind of ridiculous in a space fantasy series.
Continuity mistake: Satine and her guards along everyone else who entered the shuttle at the end of the episode disappear - you can easily see inside the shuttle and through the other window.
Continuity mistake: When Obi-Wan duels Grievous on the bridge of his Arquitens cruiser, the cyborg General slashes up several computer consoles with some of his four lightsabers. Later, when Obi-Wan sends two clone officers to the bridge to try to detach the ship, the consoles are in the background with no visible damage.
Continuity mistake: When Rex is giving orders to the heavy cannons after the super-tanks emerge, his kama is missing.
Continuity mistake: Plo's lightsaber vanishes from his belt between shots when he takes Boba over to Hondo to see if the pirate can persuade the boy to reveal the location of the hostages. (00:19:05)
Deliberate mistake: Pre Vizsla's appearance in the hologram doesn't match up with his appearance in the previous and succeeding episodes, as he's wearing clone armour covered with a cloak that has a different symbol on it. This is because when this episode was being produced, Vizsla's final character model wasn't complete yet. (00:16:25)
Continuity mistake: When Mixer and Redeye are first seen patrolling the Coronet's hold, their armour markings are visible in the first shot, but in the second, their armour is suddenly plain. (00:01:42)
Continuity mistake: After the newsreel, the episode's opening scene is of Grievous seeing Republic ships flying in to land and declaring that he needs to find an escape pod. But only in his second scene in the episode is Grievous informed that the transmitter on his escape pod is broken, prompting him to make that decision. (00:01:25)
Continuity mistake: When Mace and Ponds have the exchange that ends with the Jedi General dropping "I have a bad feeling about this", Ponds' kama (kilt) has a blue border instead of the usual maroon to match his armour. (00:08:43)
Continuity mistake: Ahsoka is wearing a red bodysuit for most of the episode, but when she falls to the floor after Bane shocks her unconscious, her legs are miscoloured a pale pink. (00:13:21)
Continuity mistake: When the Chancellor is being briefed on The Zillo Beast, Rex's kama is missing. (00:14:12)
Continuity mistake: When Padmé and Bail are walking down the hall after the Senate vote, the top of her right sleeve is miscoloured, with the purple section extending further down than it should on that outfit. (00:21:02)
Revealing mistake: When Ahsoka and Master Sinube are on their way to Ione Marcy's apartment, Ahsoka's sash keeps clipping through the bottom of her skirt. (00:09:25)
Continuity mistake: During the opening briefing with Palpatine, Mace Windu and Yoda, Luminara Unduli attends via hologram. But during the shots where Obi-Wan is explaining the attack plan, and the shot over the shoulder of Palpatine's hologram looking at Obi-Wan and Ki-Adi-Mundi, Luminara is shown as being physically present (i.e. not a blue, translucent hologram). After Palpatine, Mace and Yoda sign off, she's back to being a hologram. (00:02:00 - 00:02:30)
Continuity mistake: After the first encounter with the zombie Geonosians, it's shown there are four clone troopers in the group when they retreat. When Obi-Wan orders two of the clones to try and head back to the surface to get reinforcements, there are suddenly several more clones present. (00:11:32)
Senate Spy - S2-E4
Continuity mistake: When Padmé accesses the holo-table with the droid factory plans, she puts her clutch purse on the edge of the table. After she guesses the correct password, the purse is absent from a shot facing her as the hologram activates, but present in the next shot. (00:15:56)