Old tree root holes under foundation footing

I've been clearing an area alongside the house that we use as a gardening work area, preparing to put in new ground covering. I discovered some sinking areas near the wall, and after some digging out found that they are old holes left by the roots of a long-gone tree (there are some small moldy fragments of wood but there are otherwise empty holes). There is a hairline crack in the stucco over the area of the holes, but the foundation looks undamaged. I've been under the house and found nothing wrong on the inside. How should I go about filling these? (I can poke a stick at least three feet down a couple of these). I have a quantity of rough gravel at hand, would it be adequate to pack it in with a gravel / soil mixture? That's my first thought anyway.