Well, like I said, it doesn't always work, but sometimes it does remove the duplicates (i.e., gets rid of all the additional entries), or sometimes it gets rid of enough of them in the area of the tree I'm interested in that it works good enough for me. All I can say is next time it happens, try moving the focus to another person.
Note, however, that with intermarriages it's often necessary to duplicate people because they do in fact appear on more than one branch, and interconnecting lines from one end of the tree to another would be a mess. I think this is what Ancestry.com is trying to do when this happens, but it never seems to work right for me. My family view often looks more like a tangled skein than a tree.