Retirement tax questions

 I don't want to convert the whole Traditional IRA to a Roth (well I'd like to, but can't afford to). Sounds like I HAVE to amend my 2019 return to a non deductible contribution to my IRA and I will just lose the tax free withdrawal benefit that I would have had if it had gone into the Roth as it was intended.  Is there typically a penalty involved in this? 

My broker said there is nothing they can do on there end by the way.