I had this expenience before many time since I was
shipping more then 10 Years under one of Japanese
Company.
In this case, you can explained all to your customer / boss thru' e-mail directly (c.c. to in-charge sales) if this is nominated shipping co. by customer. Therefore, everyone know what's happen and let customer to complaine to the shipping line's sale.
Agreed with GIGI, You must send all clear reason / required to sales (C.C. To customer and your boss too). Then, everyone will know all situation and no more excuse to challenge you any more. Be careful!
shipping are easy to get "咩 Watt" and suggested you to made "Black & White" to everyone in future.