This usually happens (maybe always, I can't think of another example) when someone marries a person who is already in the family tree. The way you fix this is by deleting the "duplicate" person in one of the spots. It doesn't matter which one, pick the one that makes the least work for you. Then add them back as a partner using the choice that is worded like, "Patner with person already in tree". That will give you a dropdown where you can select the correct person.
You will still get a visual indication "(duplicate)" in both places in the tree where that person appears, but that is not an error. It's just an indication that they are related in two different ways.