I think it's definitely ambiguous, even to native English speakers. I don't see anything in the story that would lead Alma to doubt Ennis's love for the girls (other than being unfaithful to their mother, of course), so I tend to interpret it as either disappointment that she is left off the list of who he loves to pieces, or maybe even happiness that he does love them to pieces. One of my happiest things is when I see how much my husband and other loved ones adore my daughter.
The fact that her mouth twitches, but she doesn't say anything is also what Alma does. There's an awful lot she never says in their marriage, including something as important as "Stop fucking me in the butt, I don't like it." She doesn't speak up.