When you completed the "fixed files" back in March and sent them the 1095-A & 8962 I bet you didn't look at the 1040 again ... if you did then you would have seen the change to the refund amount due to the excess premium tax credit that you had to pay back ... if you had you would not be so surprised now.
Look at the form 1040 page 2 line 46 and the form 8962 to see how the credit works. If you had told the ACA you expected to make $X for the annual income so the advance credit was based on that amount. But you made X + $$$ then you got too much of the premium tax credit in advance and you have to pay back the excess on the return. You were supposed to alert the ACA during the year if the amount of income you actually made was different from what you expected so the credit could have been adjusted during the year so it was not a big shock on the return. Sadly no one reads the fine print and many people have gotten the sticker shock.
