Example document:

{
  _id: ObjectId("123"),
  array: [
    {
       _id: ObjectId("456")
    }
   ]
}

The following query doesn't work:

let find = {_id: new ObjectID("123")};
let update = {$pull: {'array._id': new ObjectID("456")}};
collection.updateMany(find, update);

The output is: cannot use the part (array of array._id) to traverse the element

If we change the update query to:
let update = {$pull: {array: {_id: new ObjectID("456")};}}
Everything works as expected.