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

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.

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

For more information, check: irs.gov