Why was Homura late?

When Madoka was about the be killed by a witch Homura was not there to help her and Sayaka had to step in to save her last minute.

At first I thought that Homura knew that she would be saved by Sayaka as she had done it in the past, but when Homura shows up she seems surprised that Sayaka was a magical girl so it makes me wonder why she was late. Did something happen that was unexpected on this timeline?

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