5818B CA FTB - Ignored withholding?

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?