I am asking her for all the details as no 5498 was provided. Ended up one contribution was not even a  ROTH IRA but a Traditional IRA so don't have to worry about that one.

One was ROTH however. 

I did google search yesterday quite a bit and found many articles, however the main question I can't find any information on is - does one needs to amend the returns just to file 5329 to pay penalties or 5329 can be filed as "stand alone"?!