This issue is typically due to your country jurisdiction start date in Avalara, so your first step will be to log into your Avalara account and check the date.
Next, compare that date to the date of the invoice which included the refund. If the jurisdiction date in Avalara is before the date of the invoices, then this is expected behavior.
We will apply tax to refunds on invoices which are dated after the country jurisdiction start date in Avalara. So if the invoice you refunded is dated 5/10, for example, and it did not have tax, and your SG entity start date is 5/1, we will tax the refund and this is expected.
To rectify this, you can alter the jurisdiction start date for that entity in your Avalara account.