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: 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: 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: 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: 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.skater49th
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 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: At the end, when R2-D2 and C-3PO are reunited with Republic forces, Master Plo asks Commander Wolffe if he knows these droids. However, Plo previously encountered R2 in both "Rising Malevolence" and "R2 Come Home" (the latter episode having the same error).skater49th
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)skater49th