Sorry to hear about the confusion; it sounds like you may have issued a refund?
When you issue a refund, we'll first look to your Square balance to cover the amount of the refund. If there aren't enough funds within your Square balance to cover your refund, Square will debit the remaining funds from your linked bank account.
I'll also note that there are no fees associated with issuing a refund, and your customer will be credited the full amount of the transaction.
Hopefully that helps clarify, let me know if that wasn't the case.
Square Community