One thing that might be going on has to do with the way that the Geni software calculates relationships. It goes the quickest way, not necessarily the direct way.
And when you are looking at profiles from the Middle Ages, there are probably several ways to get there.
So, in my case, though I'm directly descended from Llewelyn the Great through my mother, if I look at what Geni calculates, it goes through my father, and Llewelyn ends up being a cousin of an uncle or something like that.
But if I calculate it from my mother's profile, it's direct.
So you might play around with it.
If you have the direct route in your own work, walk up the line and see if the relationships are there.
If so, it's just a matter of how the software calculates. If not, then start a public discussion on the missing link, if you know that your sources are reliable.