Join 3 tables, aggregate over date field and subtract sum of two columns
This is the final query that worked, with help from Akina's comments.

SELECT
    DATE_FORMAT(s.`shipment_date`, "%m/%Y") AS `month`,
    FORMAT(SUM(u.`amount`),2) AS `net_revenue`
FROM
    (SELECT
        `amount`,
        `shipment_id`
    FROM
        `invoices`
    UNION ALL
    SELECT
        (-1 * `amount`) AS `amount`,
        `shipment_id`
    FROM
        `bills`) u
    JOIN `shipments` s
        ON u.`shipment_id` = s.`shipment_id`
GROUP BY `month`
ORDER BY `month` ASC;