Right at the end of the epi, it seemed Madoka had the idea she could contract and undo what happened to Sayaka. So I wonder if the opening was actually reality, and her wish was something like "I wish this had never happened!" thus putting them back in time. If Homera can manipulate time, maybe that is why she was unaffected. (Or her memories were.) What if ending of the show was this repeating loop and you keep wondering if they are ever going to get out of it? It would rest on Homera because she said she should have also warned Sayaka as well as Madoka.