When creating Virtual Directories for BizTalk solutions with HTTP front end, the BizTalk WCF Service Publishing Wizard is used.
This is fine, but usually you will need to move the generated web site to your solution.
If you then tried to re-create the site via a BTDF deployment, it will often fail, because the site was already created by the Wizard.
Even if it is deleted and IIS restarted this can still cause issues.
One work-around is to rename the site to something else.
Or you can delete this file: