TT is calculating a penalty for me even though my total tax due is less than $1000. Is this possible?

If you didn't make your estimated tax payments by the quarterly due dates, yes, you can still get assessed an underpayment penalty on your federal tax return. 

If you're referring to a state underpayment penalty, depending on the state the threshold for being assessed the underpayment penalty could be lower than $1,000.