The problem is that auto waypoint generation doesn't always do it right. A good example would be stairs:
stairs on Aegir mark III are not a problem, but the way i placed them on my sub
makes the auto generation create additional unnecessary waypoints that make bots move in the same spot twice before going up. I was thinking i could fix this by adjusting the points myself, but the way bots use them appears to be a bit too complicated for me. For some reason, after i made the points similar to ones in Aegir mark III, the bots would first go into the nearest room on the level and only then get back to the stairs and go up. Perhaps this is somehow related to the numbers that the waypoints have, but i am not sure.