Did you also check the box for military pay on the "Do any of these uncommon situations apply to this W-2?" screen after you entered your W-2?
You are in the Irs.gov site. This is not where military should go to file for free. Go to Turbotax.com - Click on products and pricing - then click on Military. This will bring you where you need to file for free, if you are military.
Here is the customer support contact number to work any refund issues.
This year TurboTax will recognize your W2 as Military Pay and apply the discount.