You can add a Credit to an Account in Goodbudget by entering an Expense with a negative Amount (on the Web) or by adding a transaction and changing the type of transaction from Expense to Credit (on mobile). Here's a guide in our Help Center for more details.
However, adding a Credit in this way will require you to also apply that credit to the balance of one of your Envelopes. In the case of a refund, you can simply choose the Envelope from which you originally recorded the Expense. If you'd prefer that money to stay Unallocated, you can either apply the Credit to an Envelope and use an Envelope Transfer to move the money to Unallocated, or you can add the money as an Income. Note that adding it as an Income will affect other parts of your household such as your Income vs Spending Report.