Nobody can see your clients return to tell you what is correct or not....if your client made more money that they told the marketplace insurance they would make, then its possible that they will have to payback some or all of the APTC they were given through the year.  

If you have a Sch F involved, be sure youre linking to it at the bottom of the 1095A entry screen.

You may want to see if contributing to an IRA or even a SEP IRA (since you have SE income) might reduce income enough that the payback isnt so large.

You should always double check your software computations. When all else fails, read the instructions. https://www.irs.gov/pub/irs-pdf/i1040gi.pdf