1099-R, what are all the costs incurred?

Hi to whoever can help explain. 

I had to take some money out of my 401(k) this year (2019). For the sake of this post, I'll just say it was $13,000. Of that $13k, I paid sbout $300 in state taxes and $2800 in federal. I knew that I would owe taxes  (namely, that 10% fee) on this later, and set aside enough money to cover all expenses. 

 

As I was going through my TurboTax process, the calculator at the top of the page was showing that I would be receiving a refund. This was prior to entering my 1099-R Information. (Rounded numbers for simplicity),  I was set to receive a refund of about $2,000 total. ($1,000 for each fed and state). 

 

After entering my 1099-r Info, it said I owed. I was expecting this. What I was not expecting, though, was the amount. I am confused by the math on this. Collectively, now I owe about $2,700 between fed and state. I was expecting to owe around $1300. The only additional "fee" I can see is that the state charges a fee for not having paid enough income tax (A fee of about $15). 

 

So I guess I have a few questions: 

-Are the original "returns" not factored into what I owe (because, if so, that means I would be paying nearly $5k on top of the $3k I already paid, on a $13k withdrawl).

- What other fees are added into this beyond that expected 10%? 

 

Any and all insights would be helpful - thank you!