After Madoka recreates the universe so that magical girls disappear before they become witches, there is a scene where Mami, Kyouko, and Homura come out from a battle and Kyouko is upset about Sayaka being gone.
Did Sayaka "disappear" during that fight, or did the three just come out from fighting her witch (thus Madoka not getting to Sayaka in time)?
There are, definitionally, no witches in the post-Madoka universe. As such, it is not possible that Kyouko fought Sayaka's witch.
Besides, Mami says:
行ってしまったわ。円環の理に導かれて。
ミキさん、さっきのあの一撃にすべての力を使ってしまったのね。She's gone. Taken away by the Law of Cycles.
Miki used up all her energy in that last attack, didn't she?
And furthermore, we see that they have just set a wraith/demon/魔獣 on fire. It is very clear from this that Sayaka just disappeared after running out of energy in a fight with a wraith/demon/魔獣.
