It won't. When you enter it on your Federal Return, TurboTax will automatically subtract the value of the CA MCTR on Line 8, so your Federal Adjusted Gross income excludes the MCTR payment.
If your only 1099-MISC was the MCTR, then line 8 on the 1040 should be 0, if not, it will be the sum of the other 1099s excluding the value of the MCTR payment.
Your CA return imports the Federal Adjusted Gross Income as a starting point or your income (page 2 Box 13), so it already excludes the MCTR.
So if the Federal e-file was accepted, you can go ahead and e-file the CA return too (or print them out and mail them in, whichever delivery method you normally take)
