Incorrect box sizes for items sold

[KarenFaulkner]

We sell many different sized items anywhere from a lip balm to an air fryer. Our "sample box" is set at a 12x12x12 because of the post office cubic rates. For the most part if I sell one type of item the program gets the box size pretty close. BUT if a person were to order two or more different items the program doesn't select the largest box needed , instead it selects the smallest box. Then we are having to make up the difference because the customer has already paid and we cannot charge them anymore. This can be very costly to us. 
I do watch every order and try to adjust the box size if I need to but the shipping costs have already been charged to that customer.