After you completed entry of the Form 1099-R and you had a 10% early withdrawal penalty for the 401(k), you would have come to a screen asking you to enter an exception to the penalty. If you did not enter an exception then there would not be a Form 5329 included in your tax return.
Did you have an exception as described in this IRS Tax Topic - https://www.irs.gov/taxtopics/tc558
