Goofs

When Anakin and Ahsoka exit the Twilight (approximately 1 hour and 19 minutes into the movie), Anakin is wearing the clone trooper backpack with Rotta in it. The backpack disappears several times between shots.

In the first moments of the Battle of Cristophsis scene, as Anakin, Obi-Wan, and the Clones are rushing to the defenses, one clone is firing repeatedly, seemingly at the approaching battle droids. However, as the camera switches to the separatist column, no blaster bolts can be seen, and it is unlikely that the droids are in range anyway.

Due to the limited number of models available during early production of The Clone Wars, many assets had to be reused in the background. Obi-Wan Kenobi's body was reused (complete with Jedi emblem on the shoulder) for two Gran (Ree-Yees) aliens seen in both Jabba and Ziro's palace. Similarly, Supreme Chancellor Palpatine's body was reused for two Ithorian (Hammerhead) aliens. Noticeably, these Ithorians have human hands.

The opening narration states that Jabba's son was kidnapped by a rival band of pirates. However, the television series reveals that it is actually Asajj Ventress as the true kidnapper.