Filebeat only reporting on last prospector

Elastic Stack Beats
2

In YAML terms the prospectors is a list of dictionaries. You only have one element in your prospectors list (the single - directly under prospectors). So add some dashes to create separate dictionaries for each prospector you want to define.

filebeat:
  prospectors:
    -
      paths:
        - /var/log/httpd/jf_ref.example.com_access_log
      document_type: apache
      input_type: log
      fields:
         service: apache
         type: apache_ref_access
    -
      paths:
        - /var/log/httpd/jf_ref.example.com_error_log
      document_type: apache
      input_type: log
      fields:
         service: apache
         type: apache_ref_error
    # You should also be able to put the dash on the same line as paths. 
    - paths:
        - /var/log/httpd/jf_beta.example.com_access_log
      document_type: apache
    ...