diff --git a/core/modules/migrate/src/Plugin/migrate/destination/Entity.php b/core/modules/migrate/src/Plugin/migrate/destination/Entity.php
index a91264d..4ff2016 100644
--- a/core/modules/migrate/src/Plugin/migrate/destination/Entity.php
+++ b/core/modules/migrate/src/Plugin/migrate/destination/Entity.php
@@ -128,13 +128,16 @@ protected function getEntity(Row $row, array $old_destination_id_values) {
    * @param array $values
    *   An array of destination values.
    */
-  protected function processStubValues(array $values) {
+  protected function processStubValues(array &$values) {
     $bundle_key = $this->getKey('bundle');
     if ($bundle_key && !isset($values[$bundle_key])) {
       $values[$bundle_key] = reset($this->bundles);
     }
 
-    $this->migration->set('process', array_intersect_key($this->migration->get('process'), $this->getIds()));
+    $remove_keys = array_intersect_key($this->migration->get('process'), $this->getIds());
+    foreach ($remove_keys as $key => $value) {
+      unset($values[$key]);
+    }
   }
 
   /**