3:00 - Commander Cody (to Obi-Wan): "The tracking station at Pastil is fully operational." In Return of the Jedi, Palpatine uses the same words to describe the Death Star when he tells Luke, "Now witness the firepower of this fully armed and operational battle station!" [1:41:27]
3:13 - Obi-Wan: "Don't worry, Anakin. If General Grievous comes anywhere near this quadrant, we'll know about it." "Don't worry" also appears in Attack of the Clones (Anakin tells Padmé, "Don't worry; I've given up trying to argue with you" [1:36:02]), Revenge of the Sith (C-3PO tells Padmé, "Don't worry; I'm sure he'll be alright," referring to Anakin [1:24:00], and a clone trooper tells Bail Organa, "Don't worry; the situation is under control [1:24:35]), A New Hope (Obi-Wan tells R2-D2, "Oh, don't worry; he'll be alright," referring to Luke [30:17]; Han tells Chewbacca, "Don't worry, Chewie; I think I know what he [Luke] has in mind" [1:12:12]; and Han tells Leia, "Don't worry; she'll hold together," referring to the Millennium Falcon [1:34:57]), The Empire Strikes Back (C-3PO tells R2, "Don't worry about Master Luke; I'm sure he'll be alright" [12:45], and Han tells Leia, "Don't worry" [1:20:04]), and Return of the Jedi (Lando, referring to Han, tells Nien Nunb, "Don't worry; my friend's down there; he'll have that shield down on time" [1:27:18]).
3:59 - Clone trooper (upon spotting the Separatist landing craft): "What the?" In Attack of the Clones, an alien on Coruscant also exclaims, "What the?" 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].
4:24 - Clone sergeant: "CT-327, report in. Sentry, do you copy?" Along with an occurrence of 327, there's a resemblance between these lines and what an Imperial officer says in A New Hope: "TK-421, why aren't you at your post? TK-421, do you copy?" [1:08:18]
5:21 - Clone trooper (referring to the droids): "There's too many!" A rebel pilot says nearly the same thing in Return of the Jedi (referring to TIE fighters): "There's too many of them" [1:35:13].
6:47 - Cody: "Rishi outpost, come in. Rishi outpost, come in."
Commando droid (in disguise as a clone trooper): "Sorry, commander. We're, um, experiencing technical difficulties."
Cody: "This is the inspection team."
Commando droid: "Inspection? Negative, negative, we, uh, do not require an inspection. Everything is fine here. Thank you."
Cody: "We'll be the judge of that. Prepare for our arrival."
Commando droid: "Roger, roger."
There's some similarity between this and Han's conversation with an Imperial officer in A New Hope [1:15:17].
Han: "Uh, everything's under control. Situation normal."
Officer: "What happened?"
Han: "Uh, had a slight weapons malfunction, but, uh, everything's perfectly alright now. We're fine. We're all fine here now. Thank you. How are you?"
Officer: "We're sending a squad up."
Han: "Uh, uh, negative, negative. We have, uh, a reactor leak here, uh, now. Give us a few minutes to lock it down. Uh, large leak, very dangerous."
Officer: "Who is this? What's your operating number?"
7:45 - Hevy (to the other clone troopers): "Did you hear that?" C-3PO also R2-D2 this in A New Hope [2:47].
8:33 - Cody (upon arriving at the deserted outpost): "This is not good." This is also Anakin's response in The Phantom Menace after his starfighter stalls in the hangar of the droid control ship and battle droids rush towards him: "Oops, this is not good" [1:59:01].
8:50 - Cody: "I have a bad feeling about this."
9:09 - Commando droid (in disguise as a clone trooper, to Rex and Cody): "Everything is fine and fully operational." See above, 3:00.
10:06 - Rex: "We're cut off!" While rescuing Leia in A New Hope, Luke says nearly the same thing: "We've been cut off!" [1:17:42]
10:27 - Commando droid (after an explosion, referring to Cody and Rex): "No sign of them." Luke also uses this expression during the Battle of Yavin at the end of A New Hope; after Red Ten asks Luke if he sees any fighters, Luke replies, "No sign of any- wait, comin' in point three five" [1:51:59].
13:26 - Cody (referring to Rex's plan): "This is never gonna work." In A New Hope, Han expresses similar misgivings about Luke's plan: "This is not gonna work" [1:13:51].
17:55 - General Grievous (after a battle droid tells him there are still clones at the Rishi outpost): "Then wipe them out!" Darth Sidious uses the same expression in The Phantom Menace (talking to Nute Gunray and referring to the Gungans): "Wipe them out, all of them" [1:44:52].
22:10 - Echo (to Rex): "With all due respect, sir, we failed our mission." In The Phantom Menace, Qui-Gon and Obi-Wan's pilot also says, "With all due respect" ("With all due respect, the ambassadors for the Supreme Chancellor wish to board immediately" [2:06]), and Obi-Wan says it in Revenge of the Sith while speaking to Mace Windu about Anakin ("With all due respect, Master, is he not the chosen one?" [40:32]).