The district court dismisses a complaint with leave to amend pursuant to Rule 12(b)(6), plaintiff fails to amend, and the district court dismisses the lawsuit under Rule 42(b) for "failure to follow a court order".
This is clearly an error. You're not required to amend. You can instead stand on the complaint, as plaintiff does here, and appeal.
Plaintiff files precisely such an appeal. But he argues that his complaint was improperly dismissed under Rule 12(b)(6), and ignores the fact that the district court (wrongly) used Rule 42(b).
Defendants make that point in their opposition brief on appeal, and argue the Rule 42(b) issue on the merits. Plaintiff then addresses the Rule 42(b) issue in their reply. Defendants don't ask for a further reply brief, and the issue is addressed at length at oral argument.
The majority opinion holds that plaintiff has waived the relevant (Rule 42) issue by failing to raise it in the opening brief. Judge Graber dissents, saying that she'd reach the issue, as the Ninth Circuit is clearly permitted (but not required) to do.
The majority says that defendants were prejudiced by the failure to address this issue in the opening brief. Judge Graber persuasively (in my view) responds to this issue. But I'll add one more thing to what Judge Graber says.
Defendants did not suffer prejudice not only because they addressed this issue in their opposition and at oral argument, but -- more importantly -- because they were simply flat wrong. They could have had a million pages of briefing and two years of oral argument on the issue, and all they would have done is wasted oxygen and trees. Rule 42(b) clearly doesn't apply. You're not prejudiced when you're so wrong that nothing you could have possibly said could possibly have made a difference.