check if rawDocs[key] and val are instance of Document

lib/model.js

@@ -4459,7 +4459,7 @@ function _assign(model, vals, mod, assignmentOpts) {
         }
       } else {
         if (_val instanceof Document) {
-          _val = _val._id;
+          _val = _val._doc._id;
         }
         key = String(_val);
         if (rawDocs[key]) {
@@ -4468,7 +4468,7 @@ function _assign(model, vals, mod, assignmentOpts) {
             rawOrder[key].push(i);
           } else if (isVirtual ||
             rawDocs[key].constructor !== val.constructor ||
-            String(rawDocs[key]._id) !== String(val._id)) {
+            (rawDocs[key] instanceof Document ? String(rawDocs[key]._doc._id) : String(rawDocs[key]._id)) !== (val instanceof Document ? String(val._doc._id) : String(val._id))) {
             // May need to store multiple docs with the same id if there's multiple models
             // if we have discriminators or a ref function. But avoid converting to an array
             // if we have multiple queries on the same model because of `perDocumentLimit` re: gh-9906