I don't remember a scene that had Charles & Mystique together in any of the three movies.
They didn't have too.
She tried to murder him using Cerebro in X-Men 1.
That's some gratitude for taking her in and caring for her all those years, huh?
Hell hath no fury like a woman scorned...
...and, apparently, Mystique got scorned a lot, havin' to watch Xavier hit on women at the bar all the time, and then bein' rejected by him when she was blue, nude & feelin' vulnerable.