I got help in the beat-forum here: Migrating from Filebeat 5.5.2 to 6.0.0
I had not uploaded a new beat template, after doing that, i updated the logstash.json and restarted the beat agents the errors disappeared.
Changed the logstash output to this:
index => "%{[@metadata][beat]}-%{[@metadata][version]}-%{+YYYY.MM.dd}"
Removed this from the input block: type => "log"