var Order = new Schema({
  items: [{
    product: {
      type: Schema.Types.ObjectId,
      ref: "Product",
    }
      ...
  }]
});


var Product = new Schema({
  categories: [{
    type: Schema.Types.ObjectId,
    ref: "Category",
  }]
});

Order.findById(id).populate('items.product').exec(function(err, doc) {
  var opts = {
    path: 'items.product.categories'
  };

  console.log(doc.items[0].product.categories) // [ 524f035de9d6178e460001a2, 524f0965e9d6178e460001b6 ] - these docs are in the database under the Category collection

  Order.populate(doc, opts, function(err, doc) {
    // Returns order with category array blank for each product
    console.log(doc.items[0].product.categories // []
    });
});