Write-offs and Refunds appearing as credits on customer statements

We have an issue that write-offs and refunds are appearing as credits on customer statements.  For example, we had a customer that overpaid a previous bill and refund check was issued for $661.52US. On the next billing statement, the 661.52 appeared as a credit and lower the bill to 1827.99US and it should have been 2489.52.  The math is a little off due to a .01 payment that had been previously applied.  Basically, they got refunded twice.  Same type of thing is occurring with write-offs.   It does not happened often, we have only had two cases in the past 3