A document-based app with NavigationSplitView shows duplicate file navigation controls on iPad.
This can be easily replicated by creating a multiplatform app in Xcode. The template app shows this behaviour when running on iPad.
This looks very much like a bug.
Could you open a bug report, include the description of the issue, steps to reproduce the issue and post the FB number here once you do. Bug Reporting: How and Why? has tips on creating your bug report.
I already filed a feedback:
Note the issue is evident on iOS 18.4.1 but that option wasn't available in the feedback web form.
Still the same behaviour in iOS 26 Beta
So for some undocumented reason, adding a DocumentGroupLaunchScene fixes this issue by removing the extra navigation bar.
This is causing pain for people not using NavigationSplitView: