Ein Kelokeinu isn't in my Yom Kippur Machzor, and as far as I can recall, it is not said in Shul after Musaf [or any time, for that matter]. Why is this so?
Mishna B'rura 622:5 (in my own free translation) explains the Rama's ruling that it's not said with the following explanation:
That's because on Shabas it's said to complete the discrepancy of 100 b'rachos, which is not necessary on Yom Kipur due to the plethora of praises we say. The make-up of the k'tores also needn't be said, as it's included in the avoda in musaf. But it seems it's better to say it in private so as to enumerate the spices, which are not mentioned in the avoda (Taz), and the Magen Avraham also says to say it.