I have noticed the BO pathfinding after season 4 seems to be worse now. Many times the bo's are refusing to enter doorways or having trouble when a corridor switches higher or lower via a small ramp. they dont always go to the location you request with the set rally point command.
I was playing the tears of the prophets episode in cardassian space and it was quite bad in places.
Several other missions have had this including foundry missions.
they seem to be doing the 'lets take the most direct route to follow you even if a wall is in the way', then getting stuck in and around the archways. klingon ships are pretty bad for this as there is so much junk around and door have lots of stuff around them like frames and pipes.
I can vouch for this problem as well. In the final Cardassian mission (the mission in the Bajoran Fire Caves, forgive me as I can't remember the name of it specifically), my Bridge Officers would not move anywhere, at all, unless I told them to. When i told them to go on to a bridge, they would walk straight at it, with no regard for the fire pits or the actual bridges themselves. More than half the time, they jumped right in, committing suicide.
Hardly any fun :/
I had this issue in the mission on Cardassia Prime, where you have to go retrieve the orb from them. My bridge officers had difficulties going through doorways or navigating cooridors; I had to babysit them to make sure they kept up with me and often had to run back to get one that lagged behind.