Ah, now I see. Those other resource spots are not on your current planet. Ctrl-clicking those buttons only builds all of the ones at the current planet, not at all your planets. If you go to the galaxy map and hit R, you can quickly see where you are missing resource harvesters.
As an aside, quitch, the planets are both systems and planets.
There is a single planet per system that ships happen to be at, so I kind of use them interchangeably. You're not the first to call me on it, though.