Get your taxes done using TurboTax

Sounds like you paid CA online and set it up in the TT system when you filed.  Usually this will sort itself out in the wash however the wash cycle can take several weeks or months. 

You may want to try to call them or walk into an office to get the second payment refunded...

https://www.ftb.ca.gov/aboutFTB/contact.shtml?WT.mc_id=Global_Utility_Contact

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