In ep. 10, Homura's wish is revelaed:
"I want to redo my meeting with Kaname-san. Instead of being protected by her, I want to protect her!"
This wish forced her to go back in time and re-live the month since her meeting with Madoka 100-ish times.
But in the end of the main timeline (ep.12), it is still Madoka that saves the day
by wishing to rescue all magic girls before they "completely" turn into witches.
Since the world was rebooted by Madoka's wish we briefly see events that happened during that month, such as
Sayaka's despair for being unable be with Kamijou, only to be rescued by Madoka.
I won't address the Rebellion movie in this question body, but feel free to include it in the answers.
Since by the end of ep.12 it does not feel like Homura's wish was fulfilled, question remains:
Was it fulfilled, if yes, when and how?