How can I get wood filler to match the adjacent wood when staining a floor?
The short answer is that filler isn't commonly used to repair the surface of a wood floor. It may be used to fill gaps between planks where shrinkage has occurred, or to repair holes drilled for wiring, etc., but floors are usually either sanded aggressively to remove all surface damage, or the damage is left as "character". 

You may be able to lightly dampen the areas of concern with water to check for remaining filler. Keep sanding until it's gone, then stain and seal the surface.