We all know BB-00=>Renumbered BB-28=>LOU=>Tomorrow, and Sam is actually LOU's biological father.
However one thing I don't think it is explained anywhere is, how couldn't they find this out sooner? We know in DS1 they did a very thoroughly examination and even surgery on BB-28. When Tomorrow came out from the Tar, they also did a examination on the molecular level right after, and they clearly have Sam's DNA.
In 2, it could be argued that they intentionally kept this fact from Sam, but this doesn't make sense(why?). I also remember Fragile didn't remember/realize Tomorrow is Lou until she is back to the beach. Maybe I vaguely remember a few lines said something about Sam's sperm is donated, if that's the case, I still think they should told Sam that he and Tomorrow are related(or at least DNA familiarity).
It makes even lesser sense in DS1 as there is not much hint at all. It feels like when Kojima make Sam Lou's biological father, he forgot to fill this big plot hole it create, or maybe I'm forgetting some lines?