Terminator 3: Rise of the Machines (2003)
1 plot hole
Directed by: Jonathan Mostow
Starring: Arnold Schwarzenegger, Claire Danes, Nick Stahl, Kristanna Loken, Earl Boen
Character mistake: In the opening narration, John Connor says that he was attacked by the T-1000 when he was 13 years old. This is wrong. In Terminator 2, we see that John Connor is only 10 years old, as shown on the police computer when the T-1000 accesses it. (00:02:20)
Terminator: I'm back.
Trivia: The cat lady's cat at the Animal Hospital is called Hercules. This is a tribute to Arnold Schwarzenegger who played Hercules in the 1970 movie, "Hercules In New York", his first film. (00:20:30)
Question: Why did John Connor program the Terminator to only obey Catherine's orders? Since he is the boss wouldn't he make it so the Terminator would obey his orders?
Answer: He didn't program the Terminator, she did - remember, John is dead, successfully eliminated by that very Terminator. As to why she didn't program the Terminator to obey both of them, that's an open question - possibly she needed to supply a voiceprint which obviously couldn't be obtained from the deceased John (which would also explain why the Terminator in T2 appeared to only be programmed to obey John, not both John and his mother). Alternatively, it's plausible that the Terminators can only be programmed to obey one individual, in order to prevent problems in the case of conflicting orders.
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Suggested correction: This isn't a plot hole. It's just your unfounded assumption. There's no evidence to support the supposition that the T-X has such audio detection capability.
Even if she could detect it, how could she discriminate between the sound of Catherine breathing and that of the dozens of caged animals in the room? That's stretching even fictional technology a little far.