There is an alternate ending / easter egg / deleted scene / who knows what for X-men: The Last Stand which shows the patient Charles was talking to his class of students about (the man with no high brain function) turning his head and saying Dr. Moira MacTaggert's name with Charles' voice. Moira then looks at the man and asks "Charles?". You can see the scene below. I'm assuming this is their explanation for this.
The real answer is that these movies just don't give a f*ck about continuity.
posted over a year ago
Hmmm... I don't really understand, but it's not worth it to explain me, I think...
I'll explain anyway. :) He transferred his consciousness out of his own body (the body of Charles Xavier) into the body of this patient who had no brain function. Charles took over this person's body, and it is rumored within the fandom to be the body of a brother or other family member, which could lead to some resemblance.
