Why do I owe a penalty if my employer didn't hold out enough taxes during the year?

Yes, TurboTax automatically calculates a penalty when your withholding or estimated payments and not enough to meet the requirement to pay as you go.

You can request a penalty waiver. Here's how to do that:
 

1. Sign in to your TurboTax account.
2. Select Other Tax Situations.
3. Select Start or Edit to the right of Underpayment Penalties.
4. Answer the first several screens according to your situation.
5. When you get to Penalty Waivers, answer Yes. 
6. Answer Yes to You Can Request a Waiver.
7. Answer Waive all to Do You want to Reduce Your Penalty?
8. In the explanation box enter a brief statement of why you should not have to pay the penalty. 
9. Continue through the end of the section. 
    

Penalties are determined on a quarterly basis.  If you did not have a sufficient amount of taxes withheld or paid in estimated taxes to satisfy the required amount for each tax quarter, you are subject to an underpayment penalty for the quarters where there was underpayment.

It's your responsibility to make sure that your tax withholding and estimated tax payments are sufficient to satisfy each quarter's required payment.  If the taxes withheld by your employer are insufficient you can give your employer a Form W-4 filled out appropriately to increase your tax withholding.