5:12 - Barriss Offee: "Master Windu has said we are keepers of the peace, not warriors." Barriss refers to a meeting between Chancellor Palpatine and the Jedi (including herself) in Attack of the Clones where Mace Windu says, "We're keepers of the peace, not soldiers" [4:49].
6:06 - Clone pilot (after other clones point blasters at him): "What the?" In Attack of the Clones, an alien on Coruscant makes this same exclamation as he sees Obi-Wan flying through traffic while hanging from a droid [15:08]; Han says it in A New Hope after emerging from hyperspace into a meteor shower [1:03:15]; and in Return of the Jedi, a scout trooper says this after being hit by Wicket [1:05:38].
11:50 - Ahsoka: "I have a bad feeling about this, Master Fisto."
12:42 - Ahsoka (to Rex): "Boy, am I glad to hear your voice." Luke says something similar in A New Hope: "Ben Kenobi? Boy, am I glad to see you!" [30:35]
14:06 - Anakin (to the clone troopers guarding Poggle the Lesser): "Leave us." Palpatine has similar lines twice in the movies: "Leave us" to his entourage at the opera in Revenge of the Sith [43:44] and "Guards, leave us" to the Imperial guards in Return of the Jedi [1:30:55].
18:28 - Ahsoka directs the exhaust from a hose at Barriss, similar to what Luke does to Vader in The Empire Strikes Back [1:44:37].
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There are brief cues of the Imperial March at 5:49 when Ahsoka talks about Anakin's future and at 14:02 when Anakin goes to interrogate Poggle.