As Southerners would say about the Practitioner Hotline, "bless their hearts."  Did you ask them what the difference is between a math error and a calculation error?  Maybe the idea they are trying to express is that "math error" is a technical term that embraces many entries on a tax return that have nothing to do with arithmetic.  But if you are using software, an error in arithmetic is highly unlikely.  

Form 8959 is Additional Medicare Tax.  Did your clients file joint returns?  Were the W-2s coded properly for each spouse?  I'm not sure that makes a difference, just a shot in the dark.  

Form 8960 is Tax on Investment Income.  Did your clients have any unusual items, like capital gains or S-Corp dividends?  

The one where additional Medicare tax was assessed, it was a joint return and both taxpayer and spouse had wages.  But the total wages were $258,222 resulting in $74 of additional tax.  The IRS says the additional Medicare tax was $240.  Maddening. 

On the other matter, the full refund of the Net Investment Tax calculated on the return makes zero sense.   Of course they had dividends and capital gains - that's why the 8960 was produced in the first place. 

Was there a Schedule SE with the 8959 return?  

Were these refund, or balance-due returns?  Have any refunds been paid?

Did you enter Medicare wages from the W-2s? This is often higher than Box 1 wages.

For NIIT, did the returns have K-1 business income?

And did you open the return today, to see what the software says?  (You may have to unlock it, if you lock it when filed.)

@BobKamman  Hmmm, the dreaded software update after the return was filed?  [The early worm gets eaten by a bird.]

And the bird gets eaten by a cat who gets eaten by a dog who gets eaten by an eagle who gets eaten by Sven and Ole.  It's a vicious cycle.

I have a client who received a refund on May 30th based on this error.

I just got off the phone with Practitionor Priority Service and she said there is no reference to this issue in her database. 

What are you telling clients to do? Send the money and a letter of explaination returning the erroneous refund?

Out of an abundance of curiosity, what did the IRS lady say to do with the refund after you asked her that question?

She did not say anything when I asked her about returning the refund. I asked her twice but she did not comment.