It took them three years to file and they still couldn't get it right?  Directly from the horse's mouth:

When to File

Generally, to claim a refund, you must file Form 1040-X within 3 years after the date you filed your original return or within 2 years after the date you paid the tax, whichever is later. Returns filed before the due date (without regard to extensions) are considered filed on the due date, and withholding is deemed to be tax paid on the due date. Special rules apply for refund claims relating to net operating losses, foreign tax credits, bad debts, and other issues. For more information, refer to the Instructions for Form 1040-X.