When and How was Homura's wish fulfilled?
If you are referring to how Homura can still have her wish granted in Madoka's Universe, one reason could be, as Euphoric said, it's a paradox. but then again we can say that for anything, it's more fun to see what we can infer from what we have seen, isn't it?

The second could be what I am going to call the Room of Origin (my term, not canon, since it has no name to my knowledge). We see the Room or Origin twice as being the center point of the universe being created. the first time was when Madoka recreated the universe and the second time was when Homura did it at the end of Rebellion (in Rebellion Homura says she's been there once before when the Incubator asks where they were). Since this is really ground zero for the start of the new universe we can make the assumption that a part of the old universe still exists inside the Room or Origin, serving as the basis.

The third reason could be that Homura retained her memories and abilities because she was key to creating Madoka's Universe. It was her terminating the timelines that compiles Madoka's Karmic Destiny that allowed her to become a god. In Homura's Universe Madoka regaining her memories would return her to becoming the full Law of Cycles once more and Sayaka retaining her memories initially could be because she is a part of the Law of Cycles as her secretary until Homura sealed them and probably sealed Nagisa before hand (since she did create a new life for Nagisa)