phranque - 12:04 am on Apr 26, 2012 (gmt 0)
i think you put the emphasis in the wrong place when quoting your developers' email:
I do have a goodly number of hours involved in adjusting to the redesigned PHP script, database, and associated changes plus bug hunting.
it was the associated changes that required additional bug-hunting that was not in the original scope of work.
as rocknbil said, you're lucky that wasn't more like a $7500 project in the end and your developer probably ate it at half his normal rate or less.