"But I was sure that I do not have to pay penalty for 2018 since I had withdrawn the amount by the tax deadline."
That only applies to the year in which the excess contribution was made - in this case, *2016* that had to be withdrawn before the 2016 due date (April 15, 2017). After that, the 2016 excess must be removed before the end of the next tax year (Dec. 31, 2017) to avoid the 2017 repeating penalty - the same thing applies to the 2017 excess contribution had to be removed before Dex 31, 2018 to avoid the 2018 penalty.
You now have (had) until Dec. 31 2019 to remove all excess to avoid the 2019 penalty (that you did with the 2019 distribution).
**Disclaimer: This post is for discussion purposes only and is NOT tax advice. The author takes no responsibility for the accuracy of any information in this post.**
