This is a known (and frequently reported) bug with character sheets. Any feature with the same name as a lower level feature over writes it (favored enemy, expertise, magical secrets, and ability score improvement).
I was going to purchase a D&D Beyond membership for each of my party members as a gift, but I think I'm going to pass. If they can't fix this, why should I buy them something that is broken. Pencil and paper it is I guess. That's a shame.