I just rewatched Rebellion, once again, here are some things I noticed I did not see the last time for those who care:
1. The nightmare is apparently puppeteered by magic hands, those hands are Homura's as she is the witch of the labyrinth.
2. The Ladybugs sitting on the table during the bus scene, with one of the coming to greet the other with a hat, are a reference to the tea party in "Alice in Wonderland", additionally, this is a reference to the scene where Homura is sitting in a similar fashion and drinking tea in the middle of the road. Her world is Wonderland.
3. Directly after the flower scene, Homura is talking with Kyouko who is at the Dance Machine(like here youtube.com
4. Kyouko stopped eating sticks(smoking) in Homura's barrier and world, because she no longer needs it to cope.
5. After the first time the frozen Madoka appears, it says: "Wer träumt?" - "Who dreams?" in parallel to "Wer hat geträumt?" in the end. There are too many references and mentions of dreaming for me to derive a clear meaning.
6. When Madoka, Sayaka, and Kyouko go to school, Kyouko asks Madoka to let her cheat(by copying her homework), and Sayaka states that she should not corrupt Madoka as she herself did not allow it. Yet Madoka is far more ambiguous towards it - a hint towards Madoka having far less of a problem with Homura's decision in the end then Madoka herself.
And many more subtle impressions that I can't yet put into words. I'm looking forward to my next rewatch, what will I see then?