Pug and Chihuahua

Hey! So I have a new male pug and I've had my female Chihuahua for about a year. He runs up to her and sniffs a lot and sometimes puts his paws on her back and she always yelps whenever he does any of this. (She somehow feels fine crawling over him and all of my other dogs) Is this a sexual thing that he's doing? They're both fixed and the Chihuahua was used for breeding before I got her. My pug is the sweetest in the world but I don't want him to be doing something that's scaring her or making her uncomfortable