It's not a problem specific to PS, I experience it with GIMP as well. It has to do with where you place the brush in relation to the pixels. Look at the attached, for example. The dots are all placed with the same 1x1 smooth brush. It's one of the downsides with raster-based programs like PS and GIMP. Vector-programs, like InkScape don't have this problem, because vectors are infinitely scalable.