You could edit the invoice and put $25 in the Discount field. Then go to the Comment tab on the invoice and enter a message in the Detailed Message field. For example- "A $25 discount was applied to your invoice to compensate you for the damaged pipe. We apologize for this inconvenience."
What I do is just go into the "completed jobs" tab and put in a credit there. Make sure to put in negative symbol before the actual dollar amount. Then when you generate your invoice it will generate that along with it which will be a credit