They will not move objects which are being tasked for another job. So if you have a large stone stockpile, all stones are tasked to be moved there, and you won't be able to build on top of them. You'll either have to remove your stockpile or you'll have to wait until the stone is moved there.If something like this isn't going on it's a bug of course.
Typical issue for me for what you are describing is:Order a Kitchen, Fishery and Farm Workshop... Kitchen suspended because the rock underneath it is tasked for the fishery. Similar stuff happens all the time.