This is puzzling. I'm just starting out with my store, running some tests. I ordered a product from my store through the customer-facing UI & checkout process; everything went smoothly. My personal credit card was charged and the item I ordered arrived. Now I'm testing the refund/return/exchange systems. Shopify's Orders section tells me the $1.92 was charged for California sales tax. Yet when I go to refund the order, Shopify specifies $2.51 as the tax. Why the discrepancy?
There are two tax lines for two different regions. Likely due to the shipping address and billing address being different. When you add the sum of the two tax lines, you get the $2.51 which is the correct amount of tax charged for the order.
For future test orders, I would recommend using Shopify Payments test mode or the bogus gateway as these will ensure you're not losing money on the refund process along with avoiding the account being flagged as using your own cc to purchase from yourself can be seen as fraudulent.
How have you found the setup process? Are there any other questions I can help with to get you ready for your launch?