Your libraries have a display name and an internal name in SharePoint. The internal name is what you will find in your URL and the display name is what you will see as the title of your library in SharePoint.

You migrate a site with the team site template to find that the URL of the Documents library changed from /Documents to /Shared Documents at the destination.

When the app migrates your sites, it recreates them from scratch at your migration destination. The new site will have a Documents library that has the default name Shared Documents. Since the tool merges document libraries based on their URLs, which is a reflection of their internal names, your Documents library is automatically merged into the Shared Documents library.