Ok, so to give you a rundown on the basics of the map this is happening on, it's a Starship Interior that's been constructed several hundred "units of measurement" above ground in an exterior map. The boffs generally have trouble with things like freestanding consoles and shuttles, chosing to butt up against them rather than going over or around, but the big, big issue is "Wall - Door 2", which is a Starfleet ship wall with an opening door in it. Generally, two boffs make it through, one gets stuck but can be coaxed through with waypoint/rally point thingies sometimes, and one will always become stuck on the thresh hold and unable to move past the door, or back the way they came.
Have you tried the published version of your mission?
In the editor the BOFFs always do that. Get stuck at doorways. However after publish, they act more or less normally and have little problem crossing a door.
I'd test by publishing for sure, but that may not fix it. I've had pathing problems through the door asset even on published maps. I removed most of the doors from maps in my mission "Over There" because of this very problem.
I've experianced this too, but most of the time my Boffs do quite well running around in the enviroments, other than slight little niggles like catching on things sometimes . . but then i just waypoint them like you say.
Although what i have noticed is that the problem became much worse when i trained one of my Boffs with the skill "Cover Shield" . . and when on a mission . . said boff would be forever getting caught behind his own shield . . just standing there twitching like no tomorrow trying to follow my orders to move. That was kinda weird.
I ended up retraining him in the end to use morters instead.