The weight of the shipment is always calculated as follows:
Empty box weight + Weight of all items in the return.
See here for more details on this: https://support.apphub.com/en/articles/6338366-how-is-the-total-weight-of-a-return-calculated.
1) Box weight
Usually, when you encounter a similar concern, it's prevalent that the set box weight hasn't been considered in the total weight (Return Settings >> Automatic Prepaid Labels >> Configure >> Box Weight).
Sometimes, items are shipped out in the initial outbound shipment with a box weight of 0 which is then exactly the delta in the weight and price difference.
2) Weight of items in the order (technical)
If you have a developer on your side, let them check the weight of the item on the order in question through Shopify's Order API endpoint (https://shopify.dev/docs/admin-api/rest/reference/orders/order). Shopify stores the weight of the item on the order itself as "grams". We use this data to then calculate the weight total as described above. You should always check the weight for a specific variant and update if required.
Caution: Shopify does not apply any changes you are making to the weight of an item to existing orders, only to new orders.
Note: you may encounter an error when trying to create a label if package dimensions are set to zero. If they are set to 0, no labels will be created.