I took an early distribution on my pension due to disability. The program states the early withdrawal is "tax free" but it is charging me taxes on this amount anyway

[DoninGA]

Where are you seeing the "tax free" statement when entering the Form 1099-R?

If you are under the retirement age for where you worked and the code in box 7 is a 3 then the distribution is entered on the federal tax return on Line 1h of the form 1040 as earned income.

[MayaD]

Your distribution is taxable, however, the early withdrawal penalty will be waived. 

For more information, check: irs.gov