From a quick look at a few random ways from that list, it looks like the main issue may be the use of “highway=unclassified” on roads that should be lower in the hierarchy.
For example, Way: 1227462153 | OpenStreetMap appears to be reachable only via a private service road. If the service road is itself correctly tagged, the unclassified bit can’t be a public road, so should have some other tag.