Previously when I created an XML sitemap for my home page [external links are visible to admins only] the subdomains where not included. I believe this is how it should be as I have separate sitemaps for the subdomains and have them submitted separately to webmaster tools. Now however when I create a sitemap for my home page it includes not only the subdirectories, but also includes 3 subdomains that are linked from my home page along with all their subdirectories and pages, however it records them in the sitemap in the format of subdirectories. ie: subdomain1.maindomain/ is listed as maindomain/subdomain1/.
Presently I am editing out the subdomains manually, but I am curious why this is happening and if I can change it.