diff --git a/pkg/kustomize/kustomize.go b/pkg/kustomize/kustomize.go
index 866133cf8..7d89257e7 100644
--- a/pkg/kustomize/kustomize.go
+++ b/pkg/kustomize/kustomize.go
@@ -624,11 +624,19 @@ func Inflate(
 		resources[index] = obj
 	}
 
-	for index, resource := range resources {
-		resources[index] = v1.EnsureOwnerReference(quay, resource)
+	var filteredResources []client.Object
+	for _, resource := range resources {
+		if resource == nil {
+			continue
+		}
+		filteredResources = append(filteredResources, resource)
+	}
+
+	for index, resource := range filteredResources {
+		filteredResources[index] = v1.EnsureOwnerReference(quay, resource)
 	}
 
-	return resources, err
+	return filteredResources, err
 }
 
 func operatorServiceEndpoint() string {
diff --git a/pkg/middleware/middleware.go b/pkg/middleware/middleware.go
index 74b1f11a7..09ed3ed19 100644
--- a/pkg/middleware/middleware.go
+++ b/pkg/middleware/middleware.go
@@ -7,6 +7,7 @@ import (
 	route "github.com/openshift/api/route/v1"
 	quaycontext "github.com/quay/quay-operator/pkg/context"
 	appsv1 "k8s.io/api/apps/v1"
+	autoscalingv1 "k8s.io/api/autoscaling/v1"
 	batchv1 "k8s.io/api/batch/v1"
 	corev1 "k8s.io/api/core/v1"
 	"k8s.io/apimachinery/pkg/api/meta"
@@ -221,6 +222,20 @@ func Process(quay *v1.QuayRegistry, qctx *quaycontext.QuayRegistryContext, obj c
 		return pvc, nil
 	}
 
+	if _, ok := obj.(*autoscalingv1.HorizontalPodAutoscaler); ok {
+		componentMap := map[string]v1.ComponentKind{
+			"mirror": v1.ComponentMirror,
+			"clair":  v1.ComponentClair,
+		}
+		// If the HPA is not for a managed component, return nil
+		if component, ok := componentMap[quayComponentLabel]; ok {
+			if !v1.ComponentIsManaged(quay.Spec.Components, component) {
+				return nil, nil
+			}
+		}
+		return obj, nil
+	}
+
 	if job, ok := obj.(*batchv1.Job); ok {
 		for _, oenv := range v1.GetEnvOverrideForComponent(quay, v1.ComponentQuay) {
 			for i := range job.Spec.Template.Spec.Containers {