How are you setting up the receiving end using Logstash?
The fluentd event should have two fields
log event is the log line itself and
source is either
stderr depending on which stream docker got it from. (Kontena agent follows dockers log streams).
Every line of logs should be a separate fluentd event by default. As you have a key
message in your data, my guess is that something weird happens on the parsing (Logstash?) end as KOntena does not emit events with that key.