To further clarify, this was not my error.  The client is in the 28% tax bracket and the 2018 worksheet for that tax bracket was not finalized until sometime in May, 2019, well after the tax return was filed.  The client was not accessed penalties, just tax and interest.  People have responded that the IRS is mandated by law to access interest, regardless of the cause and I thank them for their response.  I do not plan on paying the interest for this client nor are they asking me to.  

We know it's not your error, but IRS doesn't remove interest except interest on penalties. If they remove the penalties, a portion of the interest goes away too.

That's the cost of having access to $3,300 of IRS's money for several months. Not fair, I agree, but presumably they had the benefit of the funds in their possession and were using the funds for about six months. $88 isn't an unreasonable amount for using $3,300 of someone else's money for six months. I know--clients don't think too much of that line of reasoning. Nor would I, in their shoes.

IRS is adding interest onto the refunds that are being sent out due to that Sch D error, seems logical that they charge interest on the ones that ended up with a balance due.

There is no way to abate interest - it is mandated by statute.

A client's S corp just got a NJ notice with interest for installments. It is probably my fault; it is a new corp so they shouldn't owe anything, but it was $50.47. I paid it, and the client's response was "We appreciate your integrity!"

That was worth $50.47!

especially if the S-Corp learns to mind their business better.:+1:

Since you prepared and reviewed the return, it would be reasonable for you to pay the interest. It also helps to build client goodwill. You could then ask ProSeries to reimburse you, if it was a software failure.