I had a tax situation when I did a same-day sale of some nonqualified stock options. What happened is that my employer put the net gain as income on my W2. In addition, the stockbroker sent me a 1099 for the total value of the options sold. This wasn't quite correct, because the income was already reported on my W2 and the broker should have known that and not 1099'd me for it.
I filed my tax return correctly, only including the W2 income and disregarding the 1099.
The IRS added the 1099 back into my income on their end after I filed, and sent me a bill for around $190,000 for the tax on the 1099 income.
I sent them letter with a clear and correct accounting for the difference. They agreed and sent me back a letter admitting that I was correct and that my tax due was now $0.
It was a bit nerve-racking, but I'm glad they did the right thing in the end.
The California Franchise Tax Board, on the other hand, is a whole different beast. Those people are a bunch of idiotic uncouth goons.