Hi there,
If the course content you have deleted are entire resources, then all associated files should be removed along with the resource (if these files are not used elsewhere on your site).
If the files were previously embedded media files 'deleted' from currently used resources, then our FAQ on how to delete unused media files in MoodleCloud, may help provide some guidance.
If the files still appear, please contact the MoodleCloud team via the Help Widget in your Portal.
Kind regards,
Barbara