With your configuration only logs written to stdout will be collected, maybe the services that are not being collected are logging to stderr. Try to remove the stream: "stdout" line, or change it to stream: "all".
In the logs there is an error:
ERROR log/harvester.go:281 Read line error: invalid CRI log format; File: /var/lib/docker/containers/[container id]-json.log
If you continue finding this error take a look to this comment.