Your wording is a little direct. Here is how I would have written it:
"There seems to be a problem with your order. I hope we can resolve this. As you know, the FOB price that our company quoted you was for one container, but actually, your order did not completely fill a single container. As such, our price for the cargo did not go up. Our FOB charge, as you probably know, will be substantial, even though we are not shipping a full container. Since we our shipping less of our product, our company is shipping to you at a loss of profit. Our company values its customers, but in this case, we are sorry that we will have to charge you the entire cost of shipping. We hope you understand our position and if there are any further questions please do not hesitate to contact us."



