I solved the problem. Under the Virtual Directory Properties there is a application setting: 'Create Application' that was checked. I unchecked this option. I did not want this virtual directory to be its own application. That was what the problem was.
I have a asp.net web application the I publish to Plesk Onyx using FTP with Visual Studio. The website publishes fine and the website runs. I would like to add a virtual directory to a filepath under this website. example: the virtual website path www.mysite.com\apps\ would work the same as...