Turbotax is saying i paid in more on my federal income tax than is showing on my w2 and 1099. How are they figuring out how much was actually paid

You could have a foreign tax credit from investments or you could have made a typo. You may be at a screen that is including tax credits for children, car, home, etc . Review your w2 and 1099 entries. If there is still an issue, review your forms to find additional tax and credits. To see your forms:

• In desktop, switch to Forms Mode. 
• For online, see How do I preview my TurboTax Online return before filing? which includes the following two options

Look at your Form 1040.  What is the total tax on Line 24?  Do you have other amounts entered on Lines 17 thru 23?

You can view your Form 1040 plus Schedules 1, 2 and 3 at any time using the online editions. Click on Tax Tools on the left side of the online program screen. Click on Tools. Click on View Tax Summary. Click on Preview my 1040 on the left side of the screen.