Get your taxes done using TurboTax

When Form 8962 does the calculations for what Premium Tax Credit is allowed, they use the adjusted gross income for the full year. It sounds like you ended up not qualifying for as much as was estimated at the beginning of the year and was already paid out as Advanced Premium Tax Credit,so there was some repayment required. 
The only exception for this calculation is a year in which you get married, when there is an alternative calculation available. 
 

This shows the worksheet that does the calculation for adjusted gross income.