In the California interview, you should be asked about a 'waiver of underpayment penalty' where you can enter the penalty amount that was calculated. Here's more info on CA Penalties.
If you received a 1099-NEC or 1099-MISC to report your income (or neither), and you owe tax to CA, an underpayment penalty is automatically calculated.
You can mail your CA return with an explanation for the underpayment for a refund.
Yes, report the total tax to CA (including penalty) on your Resident State Return.
Here's more info on How to File a Non-Resident State Return.
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