TT says I get a refund of all my estimates, but a portion of my income is generated from CA and the FTB says I have to pay taxes on that income. I don't see how to correct what's happening in TT program
As a nonresident, you would pay tax to California on your California source income.
If the commissions you received were from services that you provided, the income is typically sourced based on where you performed the services - not necessarily where your customers are located. If the services were performed in California, you would need to allocate that income to California. If the services were performed in your home state, none of that income would be sourced or taxable to California.
On the income allocation screens within TurboTax, you will need to enter the amount of income that's subject to California tax for the program to calculate how much tax you have to pay. Note that depending on how much income you received, it's still possible that your tax liability would be zero if your state deductions are more than your income.