Does the bottom of the affordability worksheet have figures filled in? With my rough calcs, I think it should probably be filling in $2,064 in each month's box for this person, and that represents the annualized bronze-level premiums, and because that amount exceeds the % of household income, it is considered unaffordable. Did you fill out the appropriate entries in ATX to also generate the Marketplace Coverage Affordability Worksheet? That is where the annualized premium should flow from?
It seems like you've missed some input...maybe because I don't think that bottom part should be zero. That is why the program is showing the penalty, because it thinks this person can afford a premium of zero.
I'll be moving this topic over to the ACA subforum in a little while, after I know you've seen this.