Sorry, it's been over 18 months so I'm not sure what the problem with my workflow was. I suspect some failure in my extract to pull the existing data down off the server. It's hard to make sense of the errors otherwise. It looks like most of the problem ones had an existing stream but no name.

I've run a script in QGIS over the OSM data to check for intersections. I think I have fixed most of the breaks in this area (there were another 4 or 5), but need to do it by smaller area as QGIS chokes on intersecting the full Hawkesbury catchment.