Understand that there are two things happening. One is the penalty for not having insurance, and if you had coverage the entire year and answered that initial question, then you aren't being penalized.
The second thing is a little more complicated. If you received any amount of subsidy (an advance on the Premium Tax Credit) to help pay your premiums (shown on the 1095-A), then those subsidies were based on your estimated income. Now that the tax year is over and you know your actual income, the amount of PTC that you were actually eligible for is being calculated and compared to the amount you received based on your estimated income. If you estimated too low, then you have to pay some/all of that subsidy back; if you estimated to high, then you'll receive credit for an additional amount on your tax return.
That's probably what's happening in your case. You're not being penalized; you're having to pay back some of that subsidy because your income wound up being higher than your estimate.
