Zeality said it best. I hate ploy holes. As for any possible explainations I've heard:
For the Kino case: Its possible that Marle is descended from Kino, but a different woman than Ayla. The problem with this is that it is definitatly NOT what the created intended.
Doan's case is annoying. He should have ceised to exist the moment Marle time traveled to the future, the entire timeline that he exist in. The Entity excuse doesn't work here.
Maybe Lucca (she was the person who assembled them, right?) made the whole thing up. Maybe she just told them to act like being descendants and ansestors as a ruse to save Crono from going to Jail agian (or something like that, I remmber the King was going to do something to Crono, I think). But then agian, no proof.
I hate plot holes.