They probably all hold council positions and have been forbidden from going to war by their lieges.
And that's quite realistic. Only the direct vassal would have the obligation to serve personally, those below would be up to him, as long as he provided an adequate number of levies.
But unled armies are a real pain when there are leaders available.
What's the most annoying though is leaders changing between march and battle or when unloading ships or in other such "on-the-fly" situations, or when you join an ally or someone who just happens to be on the same side (e.g. because you share an enemy or are both allies of the same principal belligerent). I sometimes spend time hand-picking the leaders at the expense of not having them available with some other army and then they're still in the army but somehow are not leading.
Not the case. They'll load into individual levies, but when combine them into one army there are usually no default leaders. I think this is an error with certain government types or crown levels. Not totally sure.
Autonomous Vassals don't allow you to pick. This ends up meaning that when you get an unled levy unit (which somehow seems the norm), you still can't put your courtier in command of it. In one of my last games (France, about 170 holdings total) situation seemed to improve when I moved to Limited.