This is a quirk of OS X alias records and the Open Recent menu supplied by the application framework.
Sometimes alias records to documents get created via different paths. This happens to me most often when I create an alias to a file while connected to a file server via Airport and again while connected via Ethernet. The system sees the path to the item as different routes, and thus as different items, even though they both resolve to the same file.
It's entirely cosmetic. If it bothers you, choose the "Clear Menu" item.