It is due to some of the game logic. The Service Drones are chasing each other trying to service each other, and the inactive drones do not try to service them because they see another drone is already trying to. Elevators also cause some issues, presumably because the logic only checks if an elevator is there and not whether it is going up or down. This happens more often when a drone is trying to get to a site one level up, but there is an elevator going down on the level below it -- the drone "thinks" it can use the elevator to go up to the site, but it does not.
Since Doooooom made the source available, I plan to see if I can "fix" it and submit a patch.