I have noticed that my Bridge Officers have a difficult time going through doors. Sometimes they get stuck trying to run through the wall next to the door, or they just stand in the doorway but will not go through. I have tried using rally points, but that doesn't work.
The mission occurs in a supply depot so there are lots of crates / things in the passageways as well as in the rooms. The Bridge Officers do not seem able to run around objects very well.
This mission has not been published. It is a simple mission I am doing to learn the mechanics of mission building.
Try doing a test publish and see if that helps. Boffs can handle doors a little bit better after publish, but sometimes it just doesn't work and unfortunately there's not much you can do to fix it in that case.
Something else that might help: If there is a particular trouble spot where BOs seem to "see" the enemies on the other side of the wall, then try putting an invisible wall inside of the wall. That seems to fix it sometimes, because then the BOs don't "see" the enemies on the other side of the wall.