This issue came up after merging regions. MergeTableRegionsProcedure removes the parent regions from hbase:meta and creates HFile references in child region to the old parent regions. Running `hbck_chore_run` right after the `merge_region` will show the parent regions in "Orphan Regions on FileSystem" until major compaction is run on child region which will remove HFile references and cause Catalog Janitor to clean up the parent regions.
There are probably other situations which can cause the same issue (maybe region split?)
Having "Orphan Regions on FileSystem" list parent regions and suggest to "hbase completebulkload" is dangerous in this case as completing bulk load will lead to stale HFile references in child region which will cause its OPEN to fail because referenced HFile doesn't exist.
Figuring out these things for database administrators is tedious, so I think it would be reasonable to not consider regions with referenced HFiles to be orphans (or maybe could give an extra hint saying that it has referenced HFiles).