Adjusted 1 moth late for Excess of Contribution ROTH IRA.

After doing all my total of my 3 ROTH accounts,  I took a withdraw from one ROTH IRA account in May 2019 after I filled my 2018 tax return in April 2019.  In Feb 2020 I received the 2019  form 1099R showing a taxable amount, distribution and code J P in BOx 7.  At the time of realizing that I exceed the $5500 limit and start to withdraw, I was already 1 month late.

 

Without filing an amended 2018 return and now filling this 1099-R,  will I be penalized 10% (early withdraw before age 59) or will I be penalized 6% (excess contribution even it's only there excess of 1 month, not a whole year) ?  if so, will I get IRS letter of penalties several months later? 

any other options I have?