Retirement tax questions

Let me explain a little better. I printed up my 1040 and all the forms/worksheets after following the instructions on here as I was told.  This is where I saw my $6500 IRA distribution on line 4a and the $390 Additional tax on line 25 of form 5329(additional taxes on qualified plans including IRAs etc.) This $390 is also on line 8 on schedule 2 and line 23 on my 1040 adding $390 into my total tax due.

 

These are the steps I followed:

Under WAGES AND INCOME in TurboTax

then RETIREMENT PLANS & SOCIAL SECURITY 

IRA, 401K PENSIONS 1099-R

I filled out the 1099-R putting $6500 in Box 1 and Zero in Box 2 as I had losses on this excess contribution in my Roth. I used codes J and P and Yes, the amount I owed went down after putting in the P code making me think these steps all worked.  Nowhere did i see the question "Did you use you IRA to pay for any of these expenses" Maybe because I had no earnings?  So this tab shows $6500 on my TurboTax main screen

Under DEDUCTIONS AND CREDITS

RETIREMENT AND INVESTMENTS

TRADITIONAL & ROTH IRA CONTRIBUTIONS

I answered all the questions about the contribution and then withdrawing the contribution before I filed my taxes this year. This column on my TurboTax main screen shows 0.

 

So long story short, I'm being charged the 6% additional tax of $390 on my 1040 and wondering what I've done wrong?  

Also I am over 59 1/2 years old

I sure would appreciate any help on this