When exporting a LaTeX document in Scrivener 3, all headings include a \label{scrivauto:<$linkID>} after the header - the <$linkID> is not replaced with an actual ID for each header, so LaTeX compilers complain about repeated IDs - I’ve written a script to remove those lines, but thought maybe it was a bug or something that otherwise needs addressing. Using 2.9.0.39 Beta (838542) 64-bit on Windows 10.
Thanks for the report. The placeholder tag used to create internal hyperlinks is still in implementation.
If this were a long-term problem, we could probably devise a workaround that converted how cross-references worked. You can go through the Section Layouts pane, examining the Prefix tab, and see where these are coming from. Other approaches, such as numerical counters keyed to something unique to the item (like the title), could be a way of handling this.
But hopefully it will be fixed soon, as it looks like the ticket is under active development. And that will be nice once it is—I think this is the one remaining issue that is holding back full functionality for this template (maybe an image insertion bug still).