What is the program claiming is duplicated? 

Are you entering two of the same type of forms?

Yes I am entering two of the same form with slightly different information on it.

Duplicate 1099R

What are the forms? W-2, 1099? 

Are they from the same employer or bank? 

What is the reason you have two? 

Two 1099s.

Yes both are from the same source.

Both for making a withdraw from a 401k account. Did it two separate times. 

You can combine the amounts into one entry if the codes in box 7 are the same.