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.