When Product Options is used to affect the price of a product, it creates separate products in your store. If you set the visibility to hide these priced options from the online store, these product options will still show up on the product page and the cart page but it will show up as an inventory issue in the checkout page.
To fix this:
- From "Shopify Admin", select Products.
- Select the product you are having the issue with.
- Under "Visibility", select Manage.
- Deselect the Online Store checkbox.
- Select Save.