Contact ID 1 is an organization and causing errors
The messages about roles are verbose output from the CiviGroup Roles Sync module (civicrm_group_roles) which are logged in Drupal watchdog. Are you seeing these on screen? They don't indicate a problem, they just record which roles a user is being sync'd with and why.

I don't think it's problematic in itself that contact id 1 is an organization or that user id 1 is linked to contact id 2. The user id will not in general be the same as the linked contact id. The link is initially established based on email address and is then stored in the civicrm_uf_match table in the CiviCRM database.

Re:


  how did the "organization (default organization)" create the groups


The messages from civicrm_group_roles are saying that user 1 gets certain roles (Publish Events, Publish Jobs) because the contact that it's linked to, contact id 2 - which I assume is an Individual - is in certain groups (group ids 5, 7).