Try adding a breakpoint to your microflow, this will give you a better view of which entity is empty. Or in your case if your document will actually receive input.
Another thing is that i would guess it to go wrong in the mapping but to be sure you would have to show us your mapping/mapping microflows as well.
A NullPointerException is always bad, even if there might be something incorrect in the data, the exception should be more clear. I suggest filing a ticket with a reproduction project and we'll have a look.