If you buy the product as a CD, you are supposed to install it on your own computer and run it locally. Federal preparation and e-filing are included in the cost of the CD. State preparation is included if the box says "Federal+E-file+State" (not all boxed CDs include a state however). State e-filing is $25 extra in most states but if you prefer to save money for a slower refund, you can mail your state return.
If you are being charged for federal, it sounds like you used Turbotax Online (the web site). Turbotax Online is a different product and each tax return has a separate fee. Using the web site after you bought the CD ignores the purpose of the CD.
If you want to use the CD product, install it on your computer. Open the program and check for updates. Then you can download your online file to your computer and finish on your computer.
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