There was no contradiction. Most of the prominent Bolsheviks who happened to be Jewish were purged in the 1930s and mostly not rehabilitated until the late 1980s. So they still officially counted as enemies of the people.

Moreover, the Soviet state antisemitism, while all too real, wasn't publicly official (in the sense of antisemitic precepts being openly preached while recognized as such - a la Nazi Germany), so there was nothing to explain officially. Officially antisemitism was as illegal as any form of national hatred.

Stalin was a well-known antisemite towards the end of his life, though even he kept the likes of Kaganovich and Mekhlis around (though (x2) Kaganovich fell out of favor in the last few years of Stalin's life, together with Molotov). After Stalin's death Kaganovich was quickly discredited by Khrushchev (along with Molotov, Malenkov, Shepilov...), so he didn't have to be considered either. In fact, in one of the antisemitic Soviet books it was hinted, based on some documents, that a certain L. Kaganovich was a counter-revolutionary (this was an entirely different Kaganovich, but the book's antisemitic Communist author deliberately didn't clear this up, letting the readers draw their own conclusions - Lazar Kaganovich protested in vain).

There were certainly some Jewish Bolsheviks, who either had died early (like Moisey Uritsky), or who were indeed rehabilitated (like Iona Yakir) who were still officially honored, but, as I wrote above, this didn't have to be explained since officially it was all about "anti-Zionism", not antisemitism, and the Jewish Bolsheviks were of course anti-Zionist, like all Bolsheviks.