I happened to create a site that was named the same as one that was already in the list.
I selected the site I wanted to get rid of and when I click on delete, the action deletes BOTH of the entries.
I did a test and created two sites with the same name and then renamed one of them. That action works fine, I ended up with two sites each with a different name. I can then delete one of the sites without deleting the other.
That is the work around, but it probably isn't suppose to work the way it does.
Vince