When I pulled my retirement early, about %20 was taken off the top. I don't understand why another %10 is now being taken off when filing taxes. Any ideas?

If you took an early retirement withdraw, it is subject to both regular income taxes and a 10% penalty.  So, depending on how much your withdraw was and how much other income you have, this 20% may have just covered your regular income tax liability and not your 10% penalty on early withdraw.  

If you took the distribution to cover medical expenses or other qualified early withdraw reasons, be sure you go all the way through the interview section after you enter your 1099-R and answer the ALL of the questions related to waiver of penalty for early withdraw.  

If you have already left this section, you can go back and re-answer the questions. You can do this by 

1. Click Federal 
2. Income and Expenses
3. Scroll down and click revisit next to IRA, 401k, Pension Plan Withdrawals
4. Click continue and go back through all of the questions and answers for the retirement section.