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Labels and annotations not merging for specific resources in overlays

I'm trying to implement bases and overlays for some Kubernetes configurations that I have, but I'm running into an issue where labels and annotations are not being applied correctly to some specific resource files.

Basically, I have a base configuration consisting of `configmap.yaml`, `service.yaml`, `deployment.yaml`, `kustomization.yaml`, and `virtual-service.yaml`. These files contain common configuration settings that apply to all environments.

```yaml
# Common /path/to/project-name/base/kustomization.yaml file

apiVersion: kustomize.config.k8s.io/v1beta1
commonAnnotations:
  k8s.company/build-system: build-system.domain.tld
  # Some other common annotation that apply to all environments
kind: Kustomization
labels:
  - includeSelectors: true
    includeTemplates: true
    pairs:
      k8s.something/cost-center: group
      k8s.something.else/project: project
      # Some other common labels that apply to all environments
resources:
  - configmap.yaml
  - deployment.yaml
  - service.yaml
  - virtual-service.yaml
```

In one environment, everything works as expected. In another one, where I need to add two additional configuration files: `autoscaler.yaml` and `destination-rules.yaml`, the labels and annotations from the base `kustomization.yaml` are not being correctly to `autoscaler.yaml` and `destination-rules.yaml`, but for the rest of the files.

The `kustomization.yaml` for this environment looks like:

```yaml
# /path/to/project-name/env2/kustomization.yaml file for ENV2

apiVersion: kustomize.config.k8s.io/v1beta1
commonAnnotations:
  k8s.foo/bar: value-to-be-merged-with-the-common-ones-for-this-env
kind: Kustomization
labels:
  - includeSelectors: true
    includeTemplates: true
    pairs:
      k8s.something/environment: env2
resources:
  - ../base
  - autoscaler.yaml
  - destination-rules.yaml
```

Is there a way to resolve this issue?