When attempting to navigate or connect to a site currently being created in SharePoint, Sharegate redirects to the root site instead.
When a site is created in SharePoint, it can take a few moments before it's available to access. During this time, SharePoint will not allow any connections to the site. Sharegate will attempt to connect to this site's parent, going up the hierarchy until a successful connection is made. This is why the root site is displayed.
The solution is simply to wait until the site is completely created in SharePoint before trying to access it with Sharegate.