You are not penalized for not having health insurance if you indicated on the first screen that you had health insurance all year. The "no insurance" penalty is only activity by not indicating coverage for part of the year.
If you owe any money back, its because your Advanced Premium Tax Credit (Part III, Column C of the 1095-A) exceeded your allowable APTC. The allowable credit is based on your entire return, and the total income you made during 2016.
If you had insurance all year, make sure you indicated as much in the first screen under Health Insurance.