Conundrum with Amending my return

I already had both Federal and Michigan returns accepted. I owed tax on each return and those payments have already been electronically debited from my bank. The State payment included a $95 interest & penalty for under withholding (the importance of that will become clear).

 

I forgot to enter my wife's 1099-R for a direct rollover from a former Employers 401K to an IRA. This is not a taxable event, however I tried to start the process to amend the return but (and here is the problem) the State return keeps indicting I owe that $95 penalty which I already paid with my first e-filed return. 

This is my first Amended return and I would really appreciate some guidance with this situation. Do I even need to Amend the return since the 1099-R has no taxable event? If so, do I need to resubmit both complete Federal & State returns? How do I correct for the erroneous $95 penalty I've already paid?

 

Thank you.