No, this issue won't cause users to have to pay a penalty - if the penalty doesn't apply to them because of the IRS and California administrative decisions regarding disaster relief.
Because the Federal and state extended filing deadlines are available only for individuals living in areas impacted by official disaster declarations during specified dates, the deadlines themselves aren't updated in the software. The tax agencies made an administrative decision not to impose the penalties, but since the law itself didn't change, tax software including TurboTax still calculates the penalties.
TurboTax and other software companies are obligated to follow the law. The decision to extend filing deadlines ONLY for individuals affected by a disaster doesn't change the law, so the software calculation isn't changed.
As I stated above, if the penalty is calculated (based on the law, not the disaster relief decision), you can visit the Underpayment Penalties section of TurboTax. Go through the interview and follow the prompts; when you get to the Penalty Waivers screen, answer "yes" if you qualify for a disaster exception, then "yes" at the next screen to request a waiver of the penalty, in all or part. Enter the reason in the field provided.
If you live in a federally declared disaster area and met the special filing and payment deadlines for that disaster, you qualify for an automatic underpayment penalty waiver. Even if the penalty is calculated on the return, the IRS should not charge the penalty.
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