This was fixed with a patch from Dave.
Here was the scenario:
1) Using Shipping by Quantity Ordered.
2) Someone adds something to the cart.
3) They pick a shipping method and amount from the drop-down.
4) They then change the quantity ordered, and re-calculate the order quantity.
5) Since the shipping amount changed, it was referencing a drop-down that was no longer valid, therefore it threw the error.