I don't think Mary needed to be a mind reader. Mary may not know that Fanny doesn't really like her, but...

ch. 38
I had not, Miss Crawford, been an inattentive observer of what was passing between him and some part of this family in the summer and autumn. I was quiet, but I was not blind. I could not but see that Mr. Crawford allowed himself in gallantries which did mean nothing.”

...
Fanny shook her head. “I cannot think well of a man who sports with any woman’s feelings;

Fanny rather plainly explained her dislike of Mr. Crawford to both Edmund and Mary, which she didn't feel she could explain to Sir Thomas. Both of their responses- oh, no big deal.