I have the same problem. One of my ancestors is now showing all the same children twice and some of them are showing the same children twice.
I had this problem once before and fixed it by deleting people until the problem went away. The trouble now is that the person I think is the problem is right in the middle of my tree and I hate to think what would happen if I delete him.
I think the problem happening when I was adding census data for one of his sisters and his name came up in the additional people list - but it didn't give me an option to say it wasn't a new person or to select an existing person.