Get-SPSite Lists Our Root Site Collection Twice

Question

On SharePoint 2010 Enterprise in a 2 Server Farm (Central Admin Server + Web Front End + SQL) SharePoint returns our Root site collections twice for each host header.

Example:

Get-SPSite -Limit all


URL
___
http://intranet
http://intranet/departments/IT
http://intranet/departments/HR
http://intranet
http://MyStiesHost
http://MySitesHost/Sites/Test
http://MySitesHost

This is an issue because, some of our code and third-party code; is enumerating all Site Collections.