Trooper Chopper is supposed to have two mismatched eyes, but in some of his close-ups his eyes are the both the same color as all the other clones.
During the first scene, when Cody and Slick return, Cody is carrying a plain white clone helmet instead of his own, more elaborate version.
When Obi-Wan is explaining the Jedi's mission behind enemy lines to Cody and Rex, he first addresses Cody as a Commander, and then as Captain. This mistake arose during the editing process, as originally Obi-Wan was talking to Rex.