Freight Margin Guard

Check every carrier invoice against the orders you actually shipped, so you keep the shipping margin you charged for.

Install Freight Margin Guard from the Shopify App Store, then open it from your store admin.

Invoice reconciliation. Upload the billing export from UPS, FedEx or your LTL carrier. Every charge line is matched to the Shopify order it belongs to.
Per-shipment margin. See what you collected for shipping against what the carrier billed, order by order, in the currency you sold in.
Evidence packages. When a charge looks wrong, the app shows how it reached that conclusion and assembles the backup you need to raise it with your carrier.