WordPress database error: [Query was empty]

WordPress database error: [Query was empty]

I'm using $wpdb to connect to a different database than my wordpress one
like this:
$newdb = new wpdb(DB_NEW_USER, DB_NEW_PASSWORD, DB_NEW_NAME, DB_NEW_HOST);
I need to insert multiple rows into the database. I used the code from
this answer: Wordpress $wpdb. Insert Multiple Records.
To run the query, I use this line:
$newdb->query( $newdb->prepare("$query", $values));
When I do echo $query, this is the result: (there are more than 3 columns,
but I shortened if for times sake)
INSERT INTO table (column1, column2, column3) VALUES ('%s', '%s', '%s')
When I var_dump($values), it returns an array with the same amout of
strings as I have columns.
When I run the query, I get the following error:
WordPress database error: [Query was empty]
I tried selecting from the database in a similar fashion and it did work,
so my connected to the db is working.
What am I doing wrong?
If anyone can help me I would really appreciate it.