Issue #2186689: Fixed deletion via entity_delete().

field_collection.module

@@ -56,6 +56,7 @@ function field_collection_entity_info() {
        ),
     ),
     'access callback' => 'field_collection_item_access',
+    'deletion callback' => 'field_collection_item_delete',
     'metadata controller class' => 'FieldCollectionItemMetadataController'
   );
 
@@ -796,6 +797,14 @@ function field_collection_item_access($op, FieldCollectionItemEntity $item = NUL
   return $entity_access && field_access($op, $field, $item->hostEntityType(), $item->hostEntity(), $account);
 }
 
+/**
+ * Deletion callback
+ */
+function field_collection_item_delete($id) {
+  $fci = field_collection_item_load($id);
+  $fci->delete();
+}
+
 /**
  * Implements hook_theme().
  */