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.
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.
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)
Continuity mistake: After the shuttle has crashed, there are four surviving clones accompanying Jar Jar. From the beginning of the fight with Turk Falso's group to when they escape out of the large geyser before it goes off, the number of clone troopers keeps fluctuating between four and three, before it stabilizes back to four when they go after the pirates. (00:10:34 - 00:12:03)
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. (00:17:08)
Continuity mistake: Rex has a bandage on his left arm for the entirety of the episode after getting injured in the previous one. After Aayla destroys the probe droid, in a shot of her, Ahsoka, Rex and Bly walking over to the destroyed droid, the bandage is missing. (00:07:11)
Continuity mistake: When Obi-Wan lines up his commandeered cannon for a second shot and Waxer and Boil load in another charge, they grab the ammunition from the same exact position at the top of a stack that they took the first ammunition charge, used for Obi-Wan's first shot with the commandeered gun. (00:21:09)
Continuity mistake: Obi-Wan drops his lightsaber during the run-in with the gutkurrs, and Cody is explicitly shown returning it to him after the creatures are contained. However, when Obi-Wan initially releases his control on the creatures, the weapon is visible on his belt. (00:17:24)