Quote 43
We walk together to the kitchen. On these mornings when my brother makes breakfast, and my father's hand skims my hair as he reads the newspaper, and my mother hums as she clears the table—it is on these mornings that I feel guiltiest for wanting to leave them. (1.14)
Much like in our world, one of the main sources of guilt for Tris is her family: they seem like such perfect Abnegation folk, and it's beautiful to watch them (see "Family"), but Tris still doesn't feel like she belongs (see "Identity"). That's pretty much the perfect formula for guilt, when your family and your identity don't mesh.
Quote 44
But I have to see my parents one more time. I look over my shoulder at the last second before I pass them, and immediately wish I hadn't. My father's eyes burn into mine with a look of accusation. At first, when I feel the heat behind my eyes, I think he's found a way to set me on fire, to punish me for what I've done, but no—I'm about to cry. (6.2)
Tris's feelings of guilt might be punishment enough. Here she is, feeling all kinds of bad about abandoning her parents, to the point that she feels like she's being set on fire. The way it's phrased we know she's not: "At first[…] I think" are indicators that her first thoughts were incorrect. But still, her feeling of guilt does seem like its own punishment here.
Quote 45
My mother and father would not approve of my kicking someone when she's down. I don't care. (14.48-9)
Tris wants us to think that she doesn't care what her parents would think. But there's a big difference between kicking someone and thinking "I wonder what's for lunch today"—which shows you really don't care—and kicking someone and thinking "mom and dad wouldn't be thrilled with this." She may say she doesn't care, but the fact that she's still thinking about her parents shows that she kind of maybe sort of does.