ArenaNet has ostensibly added in these duplicate skills to add strategic depth by allowing multiple uses of the same skill. There are 5 Prophecies skills that have been duplicated in Factions for each core profession.
The following is a table of duplicate skills with the Prophecies skill listed first and the Factions skill second:
The Kurzick and Luxon skills are nearly duplicate skills. The only differences between each pair of skills are the linked title and icons. Both versions share the same name, and as such, you can only have one version of a particular skill on your skill bar at the same time.