I have a main job, but I did a freelance last year. TurboTax calculated and told me how much I owed for Self-Employment Tax. Did it just deduct this from my return?
Yes, your refund was reduced by the amount of the self-employment tax. Actually the self-employment tax is just added to your regular income tax. The total tax is paid out of the tax that was withheld from your pay, and whatever is left is your refund.