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.
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?
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.
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. (00:08:20)
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. (00:01:12 - 00:04:10)
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. 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.
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. (00:10:10)
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. (00:22:00)
Continuity mistake: When Obi-Wan Force-pushes the second droideka in the hyperdrive room, it rolls a considerable distance down the catwalk before striking an approaching squad of droids. However, in a following shot from below, the collision is much closer to where Obi-Wan was standing. (00:15:03)