The issue I have experienced is the lag time between the SS Administration updating the married name of the newly married wife.  They periodically give the IRS a file to update the IRS records with.  So waiting for the IRS and the SS Administration to sync up their details can take a couple tax return cycles, it is all about timing.   The newly married name change not in the IRS records will cause an E-file to reject in ProSeries.  So watch out for the last name change as a potential issue too. 

As for payments made by unmarried people under their own SS#'s, who will file a MFJ return, I agree - you'd think that'd be a simple 'let's match SS#'s and payments to the right return", but you may have to make a phone call to get that to happen.