I have run into problems with companion's clipping through the Unreliable and falling to their deaths causing their quests to botch. Doesn't happen often, once to Pavarti and now to Ellie. Luckily I noticed when it happened to Pavarti and was able to reload. Ellie is not so lucky.
While Ellie is alive and well, the quest still autofails as soon as I accept it. Ugh.
Still despite the few bugs I have run across, the game is in a pretty good state. I can wait until they patch it again to correct the handful of bugs. As complicated as games are now days I think its a little unreasonable to expect no flaws whatsoever on launch. I appreciate all the hard work that went into this game and the fact it wasn't monetized to hell.