Charging shipping for every package ordered in one order

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I sell a fixed dimension package and my client just ordered two of the same packages in 1 order. Shopify charged them for rate of 1 package only (Canada post). But now I have to pay double to ship the two packages to my client. (I dont combine packages I keep them separate and create different shipping labels to the same address). Can you help me understand what went wrong and how can I fix this?