The further you lean into player input into the fiction, the further you lean away from pre-plotted adventure. This is why most PbtA games specifically say not to plot anything before sessions - the fiction unfolds from player decisions. You can have threats and factions and all sorts of things, but you can't have "the Illusionist did it". The trick is finding middle ground if you don't want the full monty of PbtA.
Those NPCs in the thread above shouldn't be designed to fill a plot hole, they should be designed to fill the characters circle of people they know or know of. One of those NPCs certainly could turn out to be a bad guy, but you can't ask the characters to make the four suspects. The value of those NPCs lies in the ability of the PCs, should they find out that the prince is being framed, to have some idea who could possibly be responsible so they can take the reigns and start investigating without having to be force fed the clues.
Since this whole idea goes back to a post I made many pages ago, I'll elaborate. There's immense value in having players help write NPCs and factions. Most games that have this as a feature suggest that the NPCs in question for each character should be 'within their orbit' or people they would likely know. So the thief takes charge of writing up some stuff about the Thieves Guild or other outlaw types, A Cleric might write up some major figure in the settings religious hierarchy. There's another handle for those beyond class though, and that's background. So someone with the noble background could help write up court factions, for example. Beyond that there is family and acquaintances. Lots of room to maneuver.
Those NPCs haven't 'done anything' when they're created, they just flesh out groups and factions the character would reasonably know about. If there's intrigue or mystery afoot the players can tap those NPCs for information, or investigate them as suspects, or whatever. The key is not correlating the the player produced NPCs with GM determined plot action. In a D&D game you could design the intrigue after the NPCs, that's very cool, but you shouldn't do it before hand as it does take some of the mystery out of things.