[nebster]

I'm not sure I really understand this.

If you mean one instance in each pod, then each should be labelled differently and you can filter down to one instance.

If you mean running multiple instances in each pod (and container?), then the standard kubectl log output will also have them all joined together. For both of those, you would need to add another unique identifier to each line, or run each instance in a separate container so you can submit the logs with the pod name and container name combined being the unique identifier.