1999 taxes not filed ( IRS owes you )1000. 00 extra was withheld above taxes?Will they credit you?

By my choice in 1999 I had additional money withheld from each paycheck (above the amount already taken -single 0 0) It added up to almost $900.00 extra that should not of been sent in .I know its to late to request refund..Will the IRS apply amount that should of been refunded to a year if money was owed to them ?How can the IRS garnish wages one year when they no money was owed to that person for a previous year