Jude’s habit of covering his mouth when he smiles is indeed troubling; for one reason or another, he feels self-conscious about his body and/or his happiness. Right now, neither the reader nor Jude’s friends know anything about his past (this scene also underscores Jude’s characteristic secrecy), so it’s within the realm of possibility that he picked up this habit years back, perhaps in childhood. Regardless, at some point in time, something or someone taught Jude to hide himself from the world. Things get morally pricklier in this scene, too. JB has promised to get Jude’s consent before painting him—yet, in the novel’s present, he’s 11 paintings in already. Has JB gone back on his promise? It’s within the realm of possibility, given how selfish and driven by ambition JB is.