While deleting a site, Sharegate displays the following error:

The site cannot be deleted.

When deleting a site in SharePoint, there are many steps that happen before the actual deletion. Sharegate deletes all the subsites of the site and uninstalls all the apps in the site and all its subsites.

Sharegate will return that error if it was unable to uninstall one or more apps in the site or its subsites.

Verify if there are apps in the site or in one of its subsites. If so, try to uninstall it manually.