Get your taxes done using TurboTax

I used the calculator and input my most recent paystub information all correctly and it says that I am actually withholding more than needed per paycheck; however, last year I owed money (hundreds) in federal and state. I think this may be due to my brokerage accounts with Vanguard? How do I use the calculator to add in the returns for that?  How do I know how to use this correctly to adjust the form if the calculator is giving me information that contradicts the empirical results?