5818B CA FTB - Ignored withholding?

[mainhoon]

I had filed 2016 540X to amend my CA return as I was expecting a refund. CA sent me a 5818B where it looks like they agreed with my total tax due but then they IGNORED the tax withholding for 2016 completely (as if I never paid anything for 2016) and thus now have a $13k+ bill with penalties and fees. I don't understand how they could have missed the withholdings completely? What could be wrong?

[Rainman12]

Send FTB your copies of the 1099s and/or w-2s that show withholding in your written response to them. Perhaps their records differ - through no fault of yours ...

[Anonymous]

when you amended did you properly reflect the refund from your original return.  

[mainhoon]

Yes, the 540X clearly has a row showing withholding, the original tax owed calc, the new tax owed calc and everything is used to calculate net numbers.

I am just surprised that withholding can be overlooked! They sent me penalties, fees and the whole 9 yards as if I didn't pay anything