There's a known issue in Drupal 8 that sometimes prevents unused files from being entirely deleted.  This means that while the file may have been removed, references to the file continue to exist. This causes those file references to show over the API and, therefore, show in your FUSE content visualizations.

If you continue to see deleted files showing up at the Drupal API endpoint (and, therefore, FUSE), try one of the following methods to remove them:

  1. Install and use the File Delete module.

  2. Advanced users can remove the entries from the files_managed database table manually, using SQL or phpMyAdmin.