i'd advise against using wood filler in the cracks of a wood floor.
Those cracks shrink or grow depending on humidity, and that is why the
old filler failed. might look better for a while, but i think you will
eventually wind up with the same thing. anything you put in a place
like that would have to be flexible, and that's probably ill advised.
try ignoring them for a few months. chances are you will get used to
the ragged putty and not even notice it after a while.