It looks like you're running into this problem: Upgrade issue with Elastic Stack 5.6.0, workaround option until fix is available (there's a fix available there).
Additionally, you could migrate your existing Kibana index to 6.0, and it would work correctly in 5.6. See https://www.elastic.co/guide/en/kibana/6.0/migrating-6.0-index.html.
The problem is that, historically, Kibana wouldn't create any of the saved object mappings until the first time a given object was created. If something created a saved object outside of Kibana (like Beats, for example), the mappings it would create would be a little off. In 5.6 (or possibly 5.5, I forget when we added this...), Kibana started creating mappings on startup. The message you are seeing is because the mapping it's trying to set already exists, and isn't the same mapping that Kibana is trying to set.