To think of how not-rare it is, think of all the heterosexual child abuse that goes on within families. Child abuse is not considered rare. But how many of those abuses might result in pregnancies? Any doctor who deals regularly with young people, specifically young girls who might be pregnant, sees this regularly if they care to look. The pregnant teenager whose boyfriend "isn't around anymore" is a non-rare situation. Some subset of those are pregnant by their fathers/brothers. The problem is that asking, or performing tests that might identify the true father, may do more harm than good. So doctors don't push the matter. That doesn't mean they do not suspect what's going on.
What do you say to a girl pregnant by her brother? Termination is not a great option, the kid may well be healthy. Reporting the abuse, breaking up the household, isn't going to help either. From the doctor's perspective there isn't much they can do.