Refund data issues

Are other users and store owners still having the issue where Shopify treats returned orders as ‘refunds’ and ‘refunds owed’? This is massively skewing data when the order is actually for an exchange and/or the refund isn’t actually due (e.g. customer may accept a gift card).
We use a 3rd party app for returns and when a return is made via the portal, Shopify automatically mark it as Refund owed and all the export reports also mark it the same. The funds never seem to be rebalanced though.