Hi,
The nine is the number of relationships between the 3 people if you look at each relationship from both directions. That is why you get the 3x3 box in the clustering tool.
Your comment about the half cousin possibility is why you need to look at all the shared matches of your target people, aiming for a larger cluster. This can rule in or out certain relationships.
If your target people have significantly different relationships with other people who the should be half cousins to, for example, you can perhaps adjust the relationship between your target people.
The bigger and wider you can build your match tree the better.