I am able to reproduce the issue in my test environment. Steps to reproduce:

1. Create a deployment from Kubernetes Engine > Workloads > Deploy
2. Input your Application Name, Namespace, Labels
3. Select cluster or create new cluster

You are able to view the YAML file here and here is the sample:

---
apiVersion: "apps/v1"
kind: "Deployment"
metadata:
  name: "nginx-1"
  namespace: "default"
  labels:
    app: "nginx-1"
spec:
  replicas: 3
  selector:
    matchLabels:
      app: "nginx-1"
  template:
    metadata:
      labels:
        app: "nginx-1"
    spec:
      containers:
      - name: "nginx"
        image: "nginx:latest"
---
apiVersion: "autoscaling/v2beta1"
kind: "HorizontalPodAutoscaler"
metadata:
  name: "nginx-1-hpa"
  namespace: "default"
  labels:
    app: "nginx-1"
spec:
  scaleTargetRef:
    kind: "Deployment"
    name: "nginx-1"
    apiVersion: "apps/v1"
  minReplicas: 1
  maxReplicas: 5
  metrics:
  - type: "Resource"
    resource:
      name: "cpu"
      targetAverageUtilization: 80

After deployment if you go to Kubernetes Engine > Workloads > nginx-1 (click on it)

a.) You will get Deployment details (Overview, Details, Revision history, events, YAML)
b.) click on YAML and copy the content from YAML tab
c.) create new YAML file and paste the content and save the file
d.) Now if you run the command $kubectl apply -f newyamlfile.yaml, it will shows you the below error:

Warning: kubectl apply should be used on resource created by either kubectl create --save-config or kubectl apply
Error from server (Conflict): error when applying patch:
{"metadata":{"annotations":{"kubectl.kubernetes.io/last-applied-configuration":"{\"apiVersion\":\"apps/v1\",\"kind\":\"Deployment\",\"metadata\":{\"annotations\":{\"deployment.kubernetes.io/revision\":\"1\"},\"creationTimestamp\":\"2019-09-17T21:34:39Z\",\"generation\":1,\"labels\":{\"app\":\"nginx-1\"},\"name\":\"nginx-1\",\"namespace\":\"default\",\"resourceVersion\":\"218884\",\"selfLink\":\"/apis/apps/v1/namespaces/default/deployments/nginx-1\",\"uid\":\"f41c5b6f-d992-11e9-9adc-42010a80023b\"},\"spec\":{\"progressDeadlineSeconds\":600,\"replicas\":3,\"revisionHistoryLimit\":10,\"selector\":{\"matchLabels\":{\"app\":\"nginx-1\"}},\"strategy\":{\"rollingUpdate\":{\"maxSurge\":\"25%\",\"maxUnavailable\":\"25%\"},\"type\":\"RollingUpdate\"},\"template\":{\"metadata\":{\"creationTimestamp\":null,\"labels\":{\"app\":\"nginx-1\"}},\"spec\":{\"containers\":[{\"image\":\"nginx:latest\",\"imagePullPolicy\":\"Always\",\"name\":\"nginx\",\"resources\":{},\"terminationMessagePath\":\"/dev/termination-log\",\"terminationMessagePolicy\":\"File\"}],\"dnsPolicy\":\"ClusterFirst\",\"restartPolicy\":\"Always\",\"schedulerName\":\"default-scheduler\",\"securityContext\":{},\"terminationGracePeriodSeconds\":30}}},\"status\":{\"availableReplicas\":3,\"conditions\":[{\"lastTransitionTime\":\"2019-09-17T21:34:47Z\",\"lastUpdateTime\":\"2019-09-17T21:34:47Z\",\"message\":\"Deployment has minimum availability.\",\"reason\":\"MinimumReplicasAvailable\",\"status\":\"True\",\"type\":\"Available\"},{\"lastTransitionTime\":\"2019-09-17T21:34:39Z\",\"lastUpdateTime\":\"2019-09-17T21:34:47Z\",\"message\":\"ReplicaSet \\\"nginx-1-7b4bb7fbf8\\\" has successfully progressed.\",\"reason\":\"NewReplicaSetAvailable\",\"status\":\"True\",\"type\":\"Progressing\"}],\"observedGeneration\":1,\"readyReplicas\":3,\"replicas\":3,\"updatedReplicas\":3}}\n"},"generation":1,"resourceVersion":"218884"},"spec":{"replicas":3},"status":{"availableReplicas":3,"observedGeneration":1,"readyReplicas":3,"replicas":3,"updatedReplicas":3}}
to:
Resource: "apps/v1, Resource=deployments", GroupVersionKind: "apps/v1, Kind=Deployment"
Name: "nginx-1", Namespace: "default"
Object: &{map["apiVersion":"apps/v1" "metadata":map["name":"nginx-1" "namespace":"default" "selfLink":"/apis/apps/v1/namespaces/default/deployments/nginx-1" "uid":"f41c5b6f-d992-11e9-9adc-42010a80023b" "generation":'\x02' "labels":map["app":"nginx-1"] "annotations":map["deployment.kubernetes.io/revision":"1"] "resourceVersion":"219951" "creationTimestamp":"2019-09-17T21:34:39Z"] "spec":map["replicas":'\x01' "selector":map["matchLabels":map["app":"nginx-1"]] "template":map["metadata":map["labels":map["app":"nginx-1"] "creationTimestamp":<nil>] "spec":map["containers":[map["imagePullPolicy":"Always" "name":"nginx" "image":"nginx:latest" "resources":map[] "terminationMessagePath":"/dev/termination-log" "terminationMessagePolicy":"File"]] "restartPolicy":"Always" "terminationGracePeriodSeconds":'\x1e' "dnsPolicy":"ClusterFirst" "securityContext":map[] "schedulerName":"default-scheduler"]] "strategy":map["type":"RollingUpdate" "rollingUpdate":map["maxUnavailable":"25%" "maxSurge":"25%"]] "revisionHistoryLimit":'\n' "progressDeadlineSeconds":'\u0258'] "status":map["observedGeneration":'\x02' "replicas":'\x01' "updatedReplicas":'\x01' "readyReplicas":'\x01' "availableReplicas":'\x01' "conditions":[map["message":"Deployment has minimum availability." "type":"Available" "status":"True" "lastUpdateTime":"2019-09-17T21:34:47Z" "lastTransitionTime":"2019-09-17T21:34:47Z" "reason":"MinimumReplicasAvailable"] map["lastTransitionTime":"2019-09-17T21:34:39Z" "reason":"NewReplicaSetAvailable" "message":"ReplicaSet \"nginx-1-7b4bb7fbf8\" has successfully progressed." "type":"Progressing" "status":"True" "lastUpdateTime":"2019-09-17T21:34:47Z"]]] "kind":"Deployment"]}
for: "test.yaml": Operation cannot be fulfilled on deployments.apps "nginx-1": the object has been modified; please apply your changes to the latest version and try again

To solve the problem, you need to find the exact yaml file and then edit it as per your requirement, after that you can run $kubectl apply -f nginx-1.yaml

Hope this information finds you well.