It is possible the 1099R $2,000 withholding was not enough to cover the tax and you owe more. How old are you? You might also owe the 10% early withdrawal penalty.
It has to break out and show the 10% penalty separately on your return (schedule 2 line 6 which goes to 1040 line 23). Then you get credit for all the withholding taken out on 1040 line 25b. And by increasing your income you may lose some credits like the EIC. You can lose like up to 50% of it for taxes and penalties for federal and state.
