A duplicate person simply means that they appear more than once in a family tree because they are related in multiple ways. This is the standard way to handle multiple relationships in a computer program that generates family trees. If you were drawing the family tree by hand, you might draw lines connecting the people across generations or branches of the family. There is no easy way for a computer program to know how to do this to best convey the relationships.
In short, you don't need to do anything.