Split from this thread.
I just wanted to add to this thread to say that I'm seeing the same behavior in my SharePoint Online tenant as well. Each global nav item is duplicated, but only when viewing a "new experience" document library. Also, in my case the subsite in question does
not have the publishing feature activated, although the Publishing Infrastructure feature
is active at the site collection level.
I just created a subsite with a document library and confirmed that the duplicated nav items were shown in the new experience view for the new library. Then I deleted the subsite per instructions above, but now I'm unable to find the deleted site in the
site collection recycle bin (either in new or classic view). It's only been about 5 minutes since I deleted the site so I'll check again later this morning.