Shipping service question

I’ve been on Amazon for a few months and this is the first this has happened. All my products are custom made to order and I fulfill orders myself. I had an order placed Tuesday evening with a second day selection for shipping service. To meet a Friday delivery, I had to select expedited shipping and I ended up losing money on the order because the shipping fee charged by Amazon didn’t cover it. I have a 5 day handling time in my listing but it seems like this was overridden with the shipping service selected. How do I offer only standard shipping so this doesn’t happen?