When I run cron I get deleted nodes created again I delete products and product displays nodes type (both powered by commerce module); then all these node are gone. 

After this, I run cron and I get all those (deleted) node back in my site.

How can I trace this problem?
Have you used drupal.org/project/feeds to import content into your site? In that case perhaps you have configured your feed to make a import every time cron runs? In that case I think you should set Minimum refresh period to none.

Also, here is a thread facing the same problem: Delete feed, ron cron, feed comes back