Medieval nobles weren't out there fucking their sisters- real life isn't Game of Thrones. The closest relation allowed under medieval law in Western Europe was uncle/niece, and even that wasn't universally accepted and varied by region. Historically there are very few instances of cultures that accept marriage or sexual relationships between nuclear family members, and the exceptions are almost entirely for a small group within that society. The most prominent example in history would be the Egyptian pharaohs, who practiced brother-sister marriage at various times in history because they were believed to be gods on Earth and were expected to keep the divine blood concentrated. A normal person or even a noble in ancient Egypt would not done this- this was exclusive to the pharaohs.

So when we talk about inbreeding of medieval royal families, the main source of this is repeated first cousin marriage and marriage between uncle and niece. Both are taboo in most western societies today but are still not actually illegal in a lot of places. The biggest example of inbreeding among European noble families is Charles II of Spain, who only had 14 great great great great grandparents out of the normal 32, and he still wasn't the product of any brother-sister relationships, only cousins and uncles.