We have client X who has been charged for services. Client X was to be charged for 50% of total fee. It says that the card has been run 3 times. We need 50% payment but now it is saying that client X has not been charged at all and was refunded. Was the card “run” three times because of the refund? Does that count as a transaction?

Anything that isn’t processed in error is a transaction, including refunds.