Familial relationships in the Marvel Multiverse are notoriously prone to retcons -- just ask 616-Quicksilver, who in universe has said that he does not wish to hear from any more randos offering Yet Another Twist regarding his parentage -- but I believe that the comics versions of Xavier and the Juggernaut were a case of same-mother-different-fathers? Though it's been a while, and that could have been rewritten. Also it may have been not included in the cartoon backstory.
I remember in the flashback Marko telling Xavier that he was his step brother and that he would step all over him. However, I can't find the clip anywhere on youtube, so maybe I am misremembering.