1099R was not filed during Tax Return. What should be done to fix it?

After your return is processed and your tax liability settled amend your return. 

You should not amend until the first return has fully processed and you get the first refund or your tax due payment has cleared.  

How to Amend

https://ttlc.intuit.com/community/amending/help/how-to-amend-change-or-correct-a-return-you-already-filed/00/25588