I've had this problem too, and I've tried using console commands to move people out of my court to compensate, but the 'move' console command does not seem to be working for me. New vassals will go to their own courts but their families stay behind, when I try to move them with console commands the game does not seem to recognize the recipient court after a move command is given, I will just get a message saying "(Character name) has left your court for -----" and they stay in my court.
I know for certain I am not making mistakes with inputting the commands/character IDs because I can still use other commands I worked with (i.e. pollinate, between the same characters I am trying to move). I've used commands to banish vassals' family members who won't leave my court but their destination after that is rather random rather than with the spouses/parents they are supposed to be with, so the problem still isn't entirely fixed by that. While separated characters not having children/heirs can be worked around by using the pollinate command to get the wife pregnant, it is tedious to do, and also a little bizarre in my opinion, but if you desperately need to have 2 separated characters in your game have a kid prior to this issue being fixed, this can be a possible last resort. I'm really hoping this can be handled by the next patch, my court is clogged with vassal spouses and kids who should have left with them when I gave their families titles.