Aye, I've also noticed this. Doesn't happen when the partial construction gets a good way in, from what I can tell. Just when the construction is (almost) immediately halted due to being ready to drop (not sure if the same would happen if starting construction at 99% fatigue, would have to test). Deconstructing the partially built fence does return the stakes, though, so that works as work-around: if it tries to consume more stakes, ESC out, deconstruct and rebuild.