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Right, they're saying that the title is misleading/ ambiguous because it confuses the order of defendant and plaintiff, so if you just read Apple's motion you'd be confused about which is which and who Apple is arguing with

That's why it's important to list the parties in the correct order.

On appeals, cases are listed based on which is the appellant which is the respondent.

Yes, they’re saying it was not clear who was the defendant in the title, it seemed like the US was.