In some case, you delete products on categories but the couting for that category not updated.
I checked the database and release this SQL command to help you solve that issue.
Run this commands in PhpMySQL to solve issues.
-- clean relation terms DELETE rel FROM wp_term_relationships rel LEFT JOIN wp_posts p ON rel.object_id = p.ID WHERE p.ID IS NULL; -- Update count product_cat UPDATE wp_term_taxonomy tt SET count = (SELECT COUNT(object_id) FROM wp_term_relationships WHERE term_taxonomy_id = tt.term_taxonomy_id) WHERE taxonomy = 'product_cat';