There are two things happening when you input your health insurance information.
First, there's the determination of any penalty. Sounds like you received a waiver, so that's good.
If you're still seeing an additional amount owed, then it's probably the second thing that applies to you. When you have a policy from the Marketplace (Obamacare), you have to estimate your income when you sign up. They use that estimate to calculate how much (if any) subsidy you get to help pay your premiums (it's called the Advance Premium Tax Credit).
Then, after the end of the year when you prepare your tax return and enter the 1095-A form, they compare your "actual" income with the estimate to determine how much of the subsidy you were actually entitled to. This is where the final accounting of those subsidies takes place.
If your estimate was too low and you made more income than expected, then you'll have to pay back some of that subsidy. If your estimate was too high and you wound up earning less income than expected, then you'll receive additional credit on the tax return.
So if you had a Marketplace policy, then even though you may not have been penalized, you may have had to pay back some of that subsidy that appeared on the 1095-A.