<?php
$entity_type = "field_collection_item";
$blueprint_obj = entity_create($entity_type, array('field_name' => "field_blueprints") );
$blueprint_obj->setHostEntity('node', $order);
$blueprint_entity = entity_metadata_wrapper($entity_type, $blueprint_obj);
date_default_timezone_set("UTC");
$blueprint_entity->field_blueprint_file->file->set((array)$file);
$blueprint_entity->field_blueprint_comment = (string) $file->filename;
$blueprint_obj->save();
node_save($order);

EntityMetadataWrapperException: Invalid data value given. Be sure it matches the required data type and format. in EntityDrupalWrapper->set() (line 736 of /sites/masterprint/public_html/sites/all/modules/entity/includes/entity.wrapper.inc).

$blueprint_entity->field_blueprint_file->set((array)$file)
$blueprint_entity->field_blueprint_file->set(array('fid'=>$file->fid))