It happened to me in 3 different castles. I executed all of the nobles of the Khuzait but the (new) ruler (I decapitated her father) who got captured by one of my parties and put into my own castle. She shows up in the Lords Hall with the shackle icon and a quest, but if I try to speak to her she tells me "she's not allowed to talk to me".
Same happened later with 2 nobles from the Western Empire (shackles in Lords Hall but no quest). I just played along and some many ingame years later all three are still stuck in one of the castles owned by me. Note: They weren't there when I captures the castles, they just got put there randomly.
Unfortunately this brought my playthrough to a rather sad end, as I can't finish the quest about destroying the empire factions. They have no more lords running around and no fiefs, so I can't attack any of them and keep being stuck at about +60 war effort.
For some reason they only get put into castles or cities the player owns himself, so even trying to work around it by giving the fief to another vassal is not possible, as you can't give up fiefs (which is illogical to say the least).
Secondly: Somehow the Western Empire made peace with my kingdom, even though I didn't barter for peace. This was setting my quest progress down to -100. But apparently because their 2 last nobles are stuck as prisoners in my Lord Halls, they immediatly declared war on me again.
So I figure it is impossible to end the game as an own kingdom atm. Too much stuff is borked to oblivion true to the hashtag #8yearsdevelopment
As I still want to try out some stuff I think I will be just conquering every single faction and just keep executing every noble I take prisoner^^ Lets see how far one can take it, before the game loses its sanity and just breaks completely. There can't be a conspiracy when every single faction and minor faction is destroyed, right?
Edit: I played about 3-4h more, this lord and the two ladies are still stuck in my Lord Halls across 3 different castles. I will keep the safe and maybe play along another day to just cause havoc, but for the sake of a better start (like slightly different set of skills, early marriage and so on) I might start a new playthrough.