Can't delete the resources when enabling the prune option in K8S_PRIMARY_ROLLOUT after deleting the manifests

apiVersion: pipecd.dev/v1beta1
kind: KubernetesApp
spec:
  name: canary
  labels:
    env: example
    team: product
  planner:
    alwaysUsePipeline: true
  pipeline:
    stages:
      # Deploy the workloads of CANARY variant. In this case, the number of
      # workload replicas of CANARY variant is 10% of the replicas number of PRIMARY variant.
      - name: K8S_CANARY_ROLLOUT
        with:
          replicas: 10%
      # Wait 10 seconds before going to the next stage.
      - name: WAIT
        with:
          duration: 10s
      # Update the workload of PRIMARY variant to the new version.
      - name: K8S_PRIMARY_ROLLOUT
        with:
          prune: true
      # Destroy all workloads of CANARY variant.
      - name: K8S_CANARY_CLEAN
  description: |
    This app demonstrates how to deploy a Kubernetes app by Canary strategy without requering any mesh.\
    References: [adding a new app](https://pipecd.dev/docs/user-guide/managing-application/adding-an-application/), [app configuration](https://pipecd.dev/docs/user-guide/configuration-reference/)