I got a letter in the mail that my schedule C on my state did not match my schedule C on my federal. Doesn't turbo tax automatically plug in these numbers?

Always print a copy of your completed tax return for your records, and review it carefully before e-Filing.
You will need it if you are audited by the IRS, or to amend if a TurboTax update changes your return or for any other reason,

AND, to find your AGI next year.

 That includes your state tax returns also.

Normally yes ... but is the state correct ?    Did you amend the fed but not the state ?  Did something else happen? 

you need to tell us what items were different of Federal and State and what State.   there are legitimate reasons why for some states the Federal schedule can differ from the state. the usual cause is depreciation but it could be something else.