Hello,
if I understood correctly, the layer=1 comes from when the pier was huge bridge (https://www.openstreetmap.org/way/899814675/history); I think it could be safely removed now that it's a pier and there is only the sea below it.

The duplicate edge by OSMI overlays appears to be due to the fact that there are two man_made=pier areas with a common edge (https://blog.geofabrik.de/index.php/2019/06/14/rework-of-the-osm-inspector-routing-view/); personally, I would ignore that error given the fact that these objects seems a bit different by looking at the aerial imagery.

Happy mapping,
Marco