Try changing load order

apps/whoami/deployment.yaml

@@ -1,16 +1,13 @@
-kind: Deployment
 apiVersion: apps/v1
+kind: Deployment
 metadata:
   name: whoami
   namespace: apps
-  labels:
-    app: whoami
-
 spec:
-  replicas: 1
   selector:
     matchLabels:
       app: whoami
+  replicas: 1
   template:
     metadata:
       labels:
@@ -20,5 +17,4 @@ spec:
         - name: whoami
           image: traefik/whoami
           ports:
-            - name: web
-              containerPort: 80
+            - containerPort: 80

clusters/talos/apps.yaml

@@ -11,5 +11,4 @@ spec:
     kind: GitRepository
     name: flux-system
   path: ./apps
-  prune: true
-  wait: true
+  prune: true

clusters/talos/infrastructure.yaml

@@ -11,5 +11,4 @@ spec:
     kind: GitRepository
     name: flux-system
   path: ./infrastructure
-  prune: true
-  wait: true
+  prune: true

clusters/talos/kustomization.yaml

@@ -0,0 +1,5 @@
+apiVersion: kustomize.config.k8s.io/v1beta1
+kind: Kustomization
+resources:
+- infrastructure.yaml
+- apps.yaml