Graylog uses mongo:3 in its docker-compose image, which automatically pulls the latest production version of MongoDB, but does not set the feature compatibility version. This will cause databases created in 3.2 or earlier to fail to start in 3.6.
Per https://docs.mongodb.com/manual/reference/command/setFeatureCompatibilityVersion/, this will show the current running compatibility version and upgrade from 3.4 to 3.6:
docker exec -it mongo_container /bin/bash
mongo
db.adminCommand( { getParameter: 1, featureCompatibilityVersion: 1 } )
db.adminCommand( { setFeatureCompatibilityVersion: "3.6" } )
exit
exitWarning! Setting the featureCompatibilityVersion will prevent you from downgrading your mongo instance.