I've had factions ceasefire over alliances to me in vanilla. Allied factions at war, too, although as far as I know that only happens if they go to war after I allied them(Other times, I'm asked to choose between them. ).

I can confirm odd pathfinding issues, at least in barbarian towns. My units seem to be confused about whether they can go between buldings in areas without streets. Not sure if that happened in vanilla RTW.