Plot hole: Cato doesn't even know who Ord (the person she is impersonating) is, and yet she manages to perfectly imitate his voice and manner. She wouldn't have transformed her own internal organs, since she probably would have ruptured them.
Suggested correction: Quite apart from anything else, Cato is a member of a shapeshifting species, so why wouldn't she be able to perfectly take the form of another species? And her internal organs have nothing to do with the plot of this episode.
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.
The Academy - S3-E6
Plot hole: When Ahsoka rushes to save the students when they arrive to meet the prime minister, she attacks several secret police officers, who flee afterwards. However, we later see her standing next to the prime minister acting innocent when she pretends to side with him. The officers she fought earlier would no doubt have told Almec what side Ahsoka is really on, so her ploy never should have worked to begin with. (00:11:55 - 00:13:40)
