You get all the Orphaned or Corrupted Sites and Site collections in your SharePoint environment by using a simple powershell script that runs enumallwebs on all avaiable databases in the enviornment.
for example run ->
stsadm -o enumallwebs -databasename DBName > DBSitesFile.txt
Output these site collections into a txt file (DBSitesFile.txt) and look for the InSiteMap="False". If a site or web has InSiteMap="False" you can delete that site\web using the deletesite stsadm command.
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