I understand that once the debtor files for bankruptcy protection, a setoff (except one for income taxes allowed by an exception) is prohibited by the automatic stay. But what if the debtor has post petition debt, can the debt set off claim be filed and the funds applied?

Unfortunately, the automatic stay (11 USC §362) prevents any collection action against the debtor and, in Chapter 13, in some court’s analysis it also protects property of the debtor which would protect their assets for even the post-petition taxes. I assume this is a Chapter 13 question as it is unlikely to arise in a Chapter 7. This protection would include setoff. In Chapter 7 this is generally not an issue and you can just go ahead and submit the setoff claim.

Other courts have been more liberal and allowed the claims against the post-petition refund for post-petition debt and it really only becomes an issue if the debtor challenges it. You really need to weigh the amount and nature of your claim against the possibility of an objection, although if challenged, the decision to proceed is grounded in the law (or at least in some interpretations).