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

[KeshaH]

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.