Distributions from retirement plans. Paid penalties in 2017. The penalties were more than distributions were. But, it makes our taxes higher now even though its paid for?

Had a 401k with a previous employer. Switched jobs and did not switch 401k to new employer. Old 401k auto closed and distributed in 2016. had to pay penalties in 2017 but I have a new 401k which I make contributions to with employment check.  Since the penalties are paid do I need to input my 1099-R from 2017? (did not receive a 1099-R for 2018)