Well if the IRS changes were incorrect or your return was incorrect then you can amend your return however the penalties and/or interest paid may not be refunded but you can request it.   If the amount is significant you may wish to seek local professional assistance. 

if the stock acquisition was taxable then it's likely that tax was withheld and included on the w-2. in these situations some of the stock would have been sold to cover your share of the taxes that had to be paid.  you could check with your payroll or similar department at your company.

On Form 1040-X, IRS says: 

Ignore penalties and interest previously paid, or expected in future.

IRS will recalculate.

You can mention it in Part III that you expect your penalty to be recalculated.

@Angry11