To understand the question I'm asking, you will probably do need to watch the three Madoka Magica movies. I'll still try to avoid spoilers.
In order to fully understand the ending of the movie or rather, what happens next, I went back to look at possible clues that foreshadowed Rebellion's ending. The lyrics of Luminous by Claris, the OP for the first two movies, strikes me in particular:
My faith in saving you becoming clear
I really hope in the beginning
To bring your smile back
Make it a true miracle
The hope summoned pursued us and surpassed the world
The feeling to never give up connected our hearts before we knew it
Instead of crying, let's smile and head for tomorrow
Even if the oath we decided hurts and falls
To protect your heart
I'll be by your side
Now one thing to note is that, if I remember correctly, the song was released before the movie, although not too far apart. So it might be coincidental. However, these parts of the lyrics is interesting to me that this is exactly what Homura is doing by
taking Madoka's power to recreate the universe in order to protect her ("even if the oath we decided hurts and falls") and release her from her own perceived sufferings ("to bring your smile back").
And that she would do any lengths to protect Madoka because she still thinks she can save her("my faith in saving you..."). The second OP in the third movie has these lyrics:
You touched my heart and it shined, turning so colorful
So I'll Take Flight, Riding on Hope
Your Wishes Are Gathered Beneath the Sky That stretches Infinitely
and if I CAN go protect Them
I'll Get over the Memories of That day
WHEN I made a Promise with you and go from the Past Now
to the tomorrow that no one knows about
To me, this just described exactly what happened in the ending. In that
Everyone's memory is wiped out ("no one knows about"), Madoka's wishes to get rid of witches is also presumably granted as well, Homura turned back time for the n^100 times ("g o from the past now"), and Homura now becomes the "protector" instead of Madoka absorbing all the witches suffering ("if I can go protect them").
So does the two songs foreshadowed the ending? To me, I think that the song really did helped me to empathize with Homura despite what she did. There's more to the lyrics in my opinion, but I will keep it focused on just the ending.