After you file

Hello! I know this thread is a year old, but it came up in a Google search, so hoping someone can help!  I have a partnership that was terminated in June 2019.  I filed an extension for the Form 1065 return 3/5/20.  I filed the final return 6/9/20.  I received an IRS notice  CP162 stating the return was filed late.  Is the extension not valid because the partnership was terminated?  Should the return have been filed 90 days from June 2019?  Thank you fellow Turbo Tax community!