I replayed a couple of missions tonight (including one of mine) and the pathing problems were a thing of the past. My BO's didn't get stuck on crates, hallway furniture, or try to kill things thru walls and corners.
Also, my NPC mobs suddenly discovered their ability to wander.
Nobody shot me thru walls - but that could just have been because the mobs in the interior portion were spaced well.
I just had someone run through my mission (published on Tribble) and apparently he was able to shoot an NPC through walls but the BO pathing was better. I guess it's not a perfect fix but a hot-fix. Hopefully things will be resolved... Soon™.
I'll be sad if my twelve phaser turrets can no longer focus fire mobs through walls. But the one mission where this really matters though is the lava pit one, where all your BOs suicide within minutes of entering. Is that one fixed by this?