That first one is really giving me trouble. I think it may sometimes have to do with Lords that have negative relations with other Lords from before they joined the player faction, who then attack those other lords and start wars. I think the more common issue is that the player faction isn't actually fully implemented from what I can tell; for example, you can't use the kingdom UI to grant your own lands to a vassal; the button is grayed out saying something to the effect of "you cannot give away fiefs of the ruling clan." On top of that, we cannot yet declare war nor use the kingdom interface to attempt to make peace, yet I have seen AI factions declare war and make peace all the time. More or less, the game doesn't yet recognize that the player's clan is the ruling clan, with most of the kingdom management features currently implemented being geared towards the player being a vassal.