X-Men #9 (Page 4) & X-Men #12 (Page 13)
In both instances where Professor X says Lucifer was the one who crippled him, the margin notes say nothing of the sort. I’ve darkened the margins to make them a little easier to read.
I’M DESCENDING TO FIND LUCIFER
IF I DON’T MAKE IT - [?] X-MEN
I’M DOWN IN SUBTERRANEAN DISNEYLAND
BACK TO PRESENT - PROF AT DESK WITH HEAD IN HANDS. SURROUNDED BY X-MEN -- HE DESCRIBES SOUND - FURY - CHAOS - EXPERIENCED IN CRASH
The second of these two issues was drawn by the legendary Alex Toth with layouts provided by Kirby, which is why the margin notes are so much more in-depth.
In his A Failure To Communicate column, Mike Gartland wonders if Kirby intended to reveal in #13 that Juggernaut crippled Professor X and Lee jumped the gun in #9 (it’s likely Stan Lee’s handwriting above that says “IT WAS LUCIFER WHO CAUSED PROF X’S AFFLICTION”).
Being that Stan Lee always goes with alliterative names, “Cain Marko” is likely a Kirby creation, a fitting name for a story about a conflict between two brothers. It’d make thematic sense for Marko to be the one responsible, especially in a story title “The Origin Of Professor X!”
The origin is told in a series of flashbacks split up between a framing sequence where Juggernaut is approaching the mansion. Each flashback ends with some sort of violence or catastrophe, as if building to a big reveal. The problem is that the final flashback shows a Xavier running out of a cave-in as Marko becomes Juggernaut.
Gartland suggests that perhaps the character in the final flashback wasn’t meant to be Xavier at all, and that Xavier lost the use of his legs after the car wreck in the previous flashback. I’m not so sure, because it’d mean introducing a new character at the end of the story, who Xavier somehow heard the story from.
I don’t have access to page 12 where the car wreck happens, but the first panel of page 13 above shows him reacting to the memory of it -- the panel where he’d most likely reveal that THIS is when his legs were injured -- and the margin notes make no mention of it.
If Marko wasn’t responsible, it honestly seems like kind of a missed opportunity. The one last possibility is that maybe one of the panels of the final flashback was redrawn, and Kirby had Xavier become injured in the cave-in? Unfortunately I don’t have access to margin notes from that page, so there’s no way to confirm either way.