There's a few cases where Kruise gets "confused" regularly (also not always). The most obvious is building rail ghosts through a forest, where it sometimes refuses to remove trees marked for deconstruction, and sometimes just stops completely even though there are ghosts/trees left. Second most obvious case is when trying to revive ghosts but the player doesn't carry the required items. When it starts auto-crafting the items it often stops completely after crafting the first or second building (including subcrafts) without reviving the ghosts. It also sometimes gets stuck in a loop crafting the latest intermediate item forever. I think it also gets stuck when there is a ghost of something that can not be crafted (possibly because it's not researched yet).