You can not index data from filebeat 5.x into an index created for filebeat 6.x. You can not index data from filebeat 6.x into an index created for filebeat 5.x.
How can you tell filebeat is not forwarding to Logstash? Have you checked filebeat logs for errors? Filebeat just forwards events as is to Logstash, it is logstash finally writing the event to Elasticsearch. The document mapping (compatiblity of documents) is enforced in Elasticsearch.
You get these messages in Filebeat, Logstash or Elasticsearch? Given you configuration, the error message you posted should only come up in Logstash and/or Elasticsearch.