When you create a GKE cluster it'll come preconfigured with pushing logs to Stackdriver. And as soon as you start your application on top of GKE, logs going to stdout or stderr from your containers and will be pushed to Stackdriver Logs by Fluentd.

Severity, that you can see in Stackdriver -> Logging -> Logs viewer, depends on where event was collected. So, if your application send event to stderr you'll found it with severity ERROR at Stackdriver.

Try to check where your application send events.

EDIT You can customize Stackdriver logs with Fluentd - follow this documentation.