Do you mean you see the background but no sov in it? I have seen that before, seems totally random, and often I will see for example their mount but not the rider.
Anyway I started another game and got the same problem with the same custom sov. It's basically a Ceresa clone with clumsy and Procipinee's Crown added on, everything else is pretty much the same (except appearance), she leads Resoln not a custom faction. I've played against this leader multiple times before, have not changed anything about her, and just went and started a new game as her to make sure her file wasn't corrupted or something but it loaded fine. The fact that it happened with the same sov twice in two games probably means something, but I can't figure out what.