Nick here from Shopify.
This does sound quite strange for sure. Can I ask how you have your shipping settings set up please? Is it by price, weight of an item or do you do it by calculated shipping with a carrier? Could you also share a link to your store and I can see and take a look from the public side. It's very difficult to know what might be causing this without taking a look in the admin as it might be a multitude of things and it could be something very small. Any and all information to help troubleshoot this would be greatly appreciated.
Looking forward to hearing from you. Talk soon!
All the best, Nick