That might happen if you removed some files manually, but it's not really a problem: that list doesn't show what you have *installed*, it only shows what you can *uninstall*, but that doesn't mean you have two copies of it (they wouldn't run anyway) so, having two entires is just a cosmetic thing.
If you really want to get rid of them, because you don't like seeing two lines, just "uninstall" them both, the reinstall the Stand-Alone Addon Manager.
Note that, if you have both FSX and Prepar3D or both FSX and FS9 on the same system, it's normal you would have two entries for it and you shouldn't remove any of them.