There's a rule "Create Linked Drupal User Account" which calls the function civicrm_entity_action_create_user, which is intended to create a new Drupal user and then link it to the appropriate Civi contact. It appears that if the contact is an Organization, it will never link it. Instead it will create a new Individual and link to that.
This appears to be caused by the call to CRM_Core_BAO_UFMatch::synchronizeUFMatch at civicrm_entity.module:3056. I'm guessing at some point this function started creating a new contact if it couldn't match an existing one in the system.
Closed: won't fix
2.1
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