He never expected

I think that Sherlock loves Molly. 

I know that the ship has hit some rocky ground {The Woman, Jeannine} but look at the way he looks at her. And more than that {because he's faked that before}  I think that he always took Molly for granted. And now she's engaged and I think that jolts him a little. He came back thinking everything would be the same and while the focus is on him repairing his relationship with John I think he's just as surprised and almost as lost to find that Molly has moved on.

And as for Molly moving on hogwash. She picked a guy with dark curly hair who dresses like Sherlock and then stabbed him with a fork when he criticized Sherlock. She was the only one who saw Sherlock leave the wedding and she broke off her engagement and cared enough to yell at him in the beginning of episode three. 

Plus she's in his mind palace. And his mind palace is the place where his perception of people live. He perceives mycroft as the wise one who looks down on him, John as the one who is always there with a snarky comment, and Moriarty as the crazy, lazy, hurtful part of himself. And Molly's there too. And she's concerned about him and just wanting him to live and be ok. He knows she cares about him and we've been shown that if you care about Sherlock it shocks and touches him because he never expected anyone to care for him. Also notice that in the mind palace Molly is the only one who is nice to him.